What do you need help on? Cancel X
Close X FAQ/Walkthrough
by bluemoogle

Table of Contents

Jump to:
Would you recommend this Guide? Yes No Hide
Send Skip Hide

FAQ/Walkthrough by bluemoogle

Version: 1.00 | Updated: 08/24/10

Table of Contents

  1. Introduction
    1. About
    2. Game Version
    3. Copyright
  2. Game Basics
    1. Story
    2. Dialogue
    3. Inventory
    4. Intel
    5. E-mail
    6. Service Record
    7. Hacking Minigames
    8. Combat
    9. Stealth
  3. FAQ
    1. What are the "good" choices? What are the "evil" choices?
  4. Walkthrough
  5. Graybox (Training Operation)
    1. Escaping the Medical Facility (Find your Captors)
    2. Covert Ops Training
    3. Marksmanship Training
    4. Gadgets Training
    5. Westridge Interrogation
  6. Saudi Arabia (Operation Desert Spear)
    1. Bug Al-Samad Airfield
    2. Investigate Jizan Weapons Stockpile
    3. Intercept Nasri the Arms Dealer
    4. Intercept Shaheed and Recover Missiles
  7. Rome (Operation Deus Vult)
    1. Bug CIA Listening Post
    2. Intercept NSA Intelligence
    3. Identify Jibril AL-Bara at Chateau
    4. Contact Jibril Al-Bara / Halbech Informant)
    5. Contact Madison Saint James
    6. Investigate Marburg's Villa
    7. Investigate Delivery at Warehouse
    8. Investigate Ruins Transmission
    9. Intercept Marburg at Museum of Art
    10. Events after the Museum=
  8. Taipei (Operation True Heirs)
    1. Investigate Warehouse District Data Trail
    2. Contact Hong Shi
    3. Assault Triad Headquarters in Slums
    4. Contact Stephen Heck
    5. Retrieve NSB Data from Grand Hotel
    6. Intercept Assassination Plans
    7. Stop Omen Deng at Memorial Rally
  9. Moscow (Operation Blood Feud)
    1. Contact Grigori the Informant
    2. Investigate Weapon Shipments
    3. Assault Lazo's Yacht and Retrieve Data
    4. Contact Albatross
    5. Intercept Surkov at US Embassy
    6. Contact Surkov at Moscow Office
    7. Assault Brayko's Mansion
    8. Prevent Surkov's Escape
  10. Endgame (Operation Full Circle)
    1. Contact Scarlet Lake
    2. Contact Sheik Ali Shaheed
    3. Contact Albatross
    4. Infiltrate Alpha Protocol
  11. Appendix I: Classes
    1. Initial Classes
    2. Advance Classes
  12. Appendix II: Skills
    1. Weapon Skills
    2. Gadget Skills
    3. Defensive Skills

      ___    __      __             ____             __                   __
     /   |  / /___  / /_  ____ _   / __ \_________  / /_____  _________  / /
    / /| | / / __ \/ __ \/ __ `/  / /_/ / ___/ __ \/ __/ __ \/ ___/ __ \/ /
   / ___ |/ / /_/ / / / / /_/ /  / ____/ /  / /_/ / /_/ /_/ / /__/ /_/ / /
  /_/  |_/_/ ____/_/ /_/\__,_/  /_/   /_/   \____/\__/\____/\___/\____/_/

                            Alpha Protocol
                   Walkthrough written by Bluemoogle
                       Version 1.00 (July 2010)


Alpha Protocol, released in Summer 2010, has been advertised as one of the first espionage RPGs. Alpha Protocol can be played as an action RPG, as a third person shooter, as stealth game, or any blend in between. There is a strong emphasis on plot and characters not generally found in action/shooter games. Although the game is on the shorter side, the sheer variety of choices and non-linearity makes for multiple entertaining playthroughs.

Alpha Protocol follows secret agent Michael Thorton on his first assignment for the US secret agency, Alpha Protocol. Even after becoming a full member of the team, Agent Thorton remains in the dark about all the details of his mission. The game tells a modern tale of political conspiracy, betrayal, and regret. No matter Agent Thorton choices, there will be spilled blood and deadly consequences.

As an RPG, players are given numerous options to customize Agent Thorton, including a robust inventory and gadget system, skills to specialize in, perks for performing certain deeds, and a branching dialogue system for roleplaying a specific attitude. Loud or subtle, guns or gadgets, Agent Thorton is all about options.

This walkthrough will help you navigate the missions and complete your objective. Given the branching storyline and sheer diversity of situations you will be placed in, expect some aspects of this guide to not be relevant to every playthrough. In the most basic sense, this game can be played as a stealth game or as an action/shooter game, and this guide will help you with both play styles.

Game Version

This guide was written using the English, North American PC version of Alpha Protocol. The game is almost identical between the PC and console versions, with controls and achievements being the biggest difference. I will always reference an action by its name and not by its control button, so this guide should be compatible with all versions. Please consult the game manual for the relevant controls to your version of the game. PC users can also customize the controls in the options menu.


Copyright 2010 L.A.K. All rights reserved.

The work contained in this guide is copyrighted by the international copyright law. This document may be not be reproduced under any circumstances except for personal, private use. It may not be placed on any web site or otherwise distributed publicly without advance written permission. Use of this guide on any other web site or as a part of any public display is strictly prohibited, and a violation of copyright.

Exclusive hosting rights are given to http://www.gamefaqs.com and its affiliate site http://www.gamespot.com. No other web sites are authorized to host this guide. Please contact me at bluemoogle @gmail.com if you see this guide hosted on any other website or in any publications.

All trademarks and copyrights contained in this document are owned by their respective trademark and copyright holders.


You play as Michael Thorton, a secret agent working for a branch of the United States government that does not "officially exist." Alpha Protocol. Agent Thorton is sent to the Middle East to stop a terrorist organization, Al-Samad, from conducting a sinister plot. The game opens with a missile attack on an airplane transporting several Americans. It is later discovered that these missiles are top of their league, made by American industry! It is up to Agent Thorton to infiltrate the terrorist organization, find the missiles, determine how they were stolen, and to stop the leader of the organization from unleashing fiery hell on the world!

Sounds simple, no? What would an espionage story be without conspiracy and plot twists? It is never that simple, and Agent Thorton's mission does not end with stopping some small time terrorists. His mission takes him to the global scene of politics, and to the darkside of secret intelligence. His actions uncover an even worse plot, and he is the only one capable of stopping it. Must he save the world alone? That depends on your choices, and your tolerance of regret.

Agent Thorton's choices shape the course of history and the nature of global politics. There are multiple endings to the game, and the path to each ending can be wildly different between playthroughs. Although every agent will visit the same locations, these locations can be very different depending on your actions. Is there a group of enemies waiting to ambush you, or have you befriended them earlier, and now they will assist you in taking control of an area? Did you spare the Mafia boss and enlist the help of his goons, or did you execute the poor sap and eliminate crime from the streets?

The story is told by Agent Thorton as he recollects on his early missions. Periodically, the game will jump three months forward to show Thorton and a mysterious man discussing his decisions made during each mission. Both know the consequences of every decision, but their discussions are often shown before the player learns the truth. Of course, the two are vague when describing events not yet seen by the player, so they leave several questions open and unanswered. This will leave you, the player, guessing until the very end of what is truly going on.


Dialogue is the driving component of the storyline, and the main way you can roleplay Agent Thorton to your specificiations. The dialogue system is similar to other Western RPGs, but with a few important modifications. First, the dialogue system is timed. Every dialogue choice is given approximately 10-15 seconds for deciding the response. Sometimes this response time starts ticking while the other character is still talking, so you will need to be quick thinking and careful at listening.

Fortunately, there are some consistencies to make choosing dialogue a little easier during high stress moments. There will only be two, three, or four dialogue choices, and most often it will only be three. When only two options are given, usually it is an important plot decision, such as letting someone live or executing them.


The three and four option dialogue choices have specific moods or attitudes for each choice. These are always in the same spot on the dialogue wheel. Aggressive responses are always the top choice, sauve choices are always the left choice, professional choices are always the right choice, and special choices are always the bottom choice. These may come under different names, like "angry" instead of aggressive, "casual" instead of sauve, and "mission" instead of professional, but they maintain the same attitude and tone of voice.

The fourth special option depends on the situation. It is usually a "dossier" option, which is only available if you have enough information collected on the character. Because dossier options are harder to unlock, they usually have bigger ramifications. They are often plot changing options, and will turn foes into friends, and friends into enemies. They can initiate boss encounters, or they can let you skip them. The fourth special option is also sometimes related to your class. If you encounter a situation where technology is being difficult, and you are playing as a gadget class, you can use the fourth option to unlock a plot thread not available to the other classes. Less often, the fourth option is just a simple dialogue choice, usually with a neutral attitude. Usually the game will not offer this neutral choice (such as "silent") because there is more roleplaying potential in choosing the different attitudes.

Every character in the game responds differently to the different attitudes. In most cases, each character will have an attitude they like, an attitude they are neutral, and an attitude they dislike. These rarely change; a character that likes professional responses will almost always like professional responses, every time.

Important! Personality History:

The game not only tracks which dialogue attitudes you use during each conversation, but the attitude you use most during the game. Characters will hear about your previous attitude before you meet them, and this can alter the game. If you act aggressively most the game, characters will recognize that you are an aggressive person, even if you switch to temporarily using professional during conversations with them. Switching your attitude can surprise them, but it is not guaranteed to unlock dialogue threads previously locked by your past personality. This gameplay feature is most important if you are trying to fight the hidden boss fights, or find other secrets, since some are unlocked only with certain long-standing personalities.

Sometimes if you piss a character off, they will no longer favorably respond to the attitude they previously liked. Each character has a reputation between -10 and 10, with 0 being neutral. Attitudes that work favorably between 0-10 may not work favorably if the character dislikes you. Keep this in mind if you are purposefully trying to make friends, or purposefully trying to make enemies.There are generally more benefits to making friends instead of enemies. There are only a few special cases where being enemies can have some positive effects. This guide will point out when it's good to be friends, and when it is good to be enemies. Also, your handlers will provide different benefits depending if they like or dislike you. Sometimes the benefit from working with a hated handler is better than the benefit of working with a handler that loves you. This is more dependent on your play style.


Your inventory is where you manage your weapons, armor, and gadgets. You can carry two weapons, one set of armor, and a variable amount of gadgets to each mission. The amount of gadgets you can carry depends on the carrying space of your armor, and which skills you have. All items can either be found in the game world, or bought from the blackmarket Clearinghouse.


There are four weapon classes in the game: pistols, submachine guns (SMGs), shotguns, and assault rifles. You can carry any two weapons to a mission, but you will usually use one main weapon. The secondary weapon is most useful to characters that want to specialize in closer ranged weapons, since the secondary weapon can be reserved as a longer ranged when needed. Please see Appendix II: Skills for more detailed information on the weapons.

The four weapon classes can be upgraded with gun components: barrels, magazines, accessories, and sights. These components are specific to each class of weapon, and generally improve a specific weapon, maybe at the cost of reducing a different stat. Weapon stats include damage (aka stopping power), stability (how responsive/jittery the weapon is when aiming), accuracy (how likely the bullet will hit where the crosshair is), recoil (how much the weapon will move when firing), and magazine size (how much ammunition is carried in each clip). For most stats and weapons, a 20 is considered average.

Pistols are a versatile weapon, and the primary weapon for agents using stealth. They are the only weapon to have non-lethal ammunition (tranquilizer darts). Pistols perform best at close ranges, but an agent trained with pistols can get critical head shots on even distant targets. Pistols can also be attached with a silencer, letting an agent dispose of enemies without being detected.

SMGs are the only dual wielded weapon in the game. Fortunately an agent only needs to buy one SMG- the game automatically pairs it with an identical SMG. SMGs are fun and flashy, but they are less effective than shotguns are close ranges and less effective than assault rifles at long ranges. This leaves them without a niche, but they do have better stopping power than the assault rifle when it comes to groups of enemies.

Shotguns are the strongest weapon in melee range, and can devestate even heavily armored opponents. A close ranged headshot from a shotgun will instantly kill most enemies, even if the shot was not a critical shot. The force of the blast of a shotgun can also knock enemies down, allowing an agent to move in and curbstomp them to death.

Assault Rifles are the strongest weapon at long range, and the most effective. While shotguns and SMGs may do little to no damage to distant foes, an assault rifle can clear a room of guards from a second story balcony with ease. The assault rifle shines when the agent can camp himself in a defensive position and shoot all the enemies. Agents that prefer to run-and-gun would do better with shotguns or SMGs.

Melee or Close Quarters Combat (CQC) is not technically a weapon class. An agent cannot buy melee weapons, he can only improve his melee abilities through skills. A trained martial artist can be just as powerful as an agent trained with guns. Martial artists can also lock opponents down. This comes at the cost of needing to be in melee range, so beware of bringing "fists to a gunfight."

Stealth Attacks are a special brand of melee attacks, only usable on enemies that have not detected the agent. Non-lethal take downs do not require a weapon, but are slightly more time consuming. Lethal knife attacks require a weapon, and are faster to perform. Both lethal and non-lethal stealth attacks are instant kills/KOs, and the knife cannot be upgraded.


Any agent can equip any armor, no matter the class of agent or his skills. Likewise, any agent can use any armor components. There are three classes of armor: combat, utility, and stealth. Please see Appendix I: Classes for more information on the different archetypes. Additionally, an agent can also wear his casual clothing to missions, with the clothing being regional specific. Both the casual clothing and armor will change appearance depending on Agent Thorton's location. He does not need to re-buy the set of armor, the appearance will automatically change. For example, his armor will be golden camouflage in the desert, and the same set of armor will be solid black in dark, urban cities.

Like weapons, armor can be upgraded with components. These components may improve a stat, or they may slightly alter gameplay, such as decreasing the chance Agent Thorton is detected by electronic devices. Armor stats include endurance ("shields" in other games), damage reduction, upgrade slots, inventory capacity, and sound dampening.

Combat armor is best suited for agents that prefer to run into a room guns blazing. It has high endurance (the most shields), but also produces the most amount of sound.

Utility armor is best suited for agents that prefer to use gadgets, or like to mix stealth with combat during the same mission. Utility armor has medium endurance and produces less sound that combat armor. Utility armor also has the most inventory space for gadgets, and the most upgrade slots.

Stealth armor is best suited for agents that prefer to hide from enemies. It provides the least amount of endurance, but it actually dampens sound.

Casual Wear provides no protection, but it is actually quieter than the early stealth armor. Sometimes an agent may want to wear casual wear during a mission if his other options are too noisy, or if he wants to legitimately appear casual. Some characters will react to an agent wearing casual clothing instead of armor.


An agent can carry special technology with him during missions. Gadgets can be healing devices, explosives, EMPs, noise generators, and other devices useful for different situations. Some agents specialize specifically in gadgets, granting them more more carrying capacity and better results when using gadgets. The game never requires gadgets, and there is no use in hoarding them. They are cheap and readily available between missions. If you have a gadget and a situation where you can use it, use it! Beware that loud gadgets will, shockingly, give away an agent's position. So be careful when using grenades and mines if you are trying to stealth.

EMP Grenades can either be thrown at electronic devices, including turrets, cameras, or simple keypads, or can be activated directly by standing next to an electronic device and pressing the appropriate button. If thrown, the EMP releases a large shock that disables near by electronic devices. If used directly, the EMP can skip the hacking minigame for the agent (this latter ability requires a skill). EMP grenades can be upgraded to improve the stun duration.

Explosive Grenades can also be thrown at targets, doing a large amount of damage. Explosive grenades can also be placed into the ground and act as proximity mines. Instead of exploding after a set amount of time, an explosive grenade placed on the ground will explode when an enemy approaches. Explosive grenades can be upgraded to improve the damage.

Incendiary Bombs work similarly to explosive grenades, except they release a large cloud of fire. This fire remains on the ground and will burn near by enemies, and any enemies that approach. Burning enemies stop attacking and will try to put out the fire, but most will die before they can. Incendiary bombs can be upgraded to improve the damage and blast radius.

Flashbangs are non-lethal grenades that stun and temporarily blind enemies. These can allow an agent to escape without being detected, though the guards will search for the agent after the flashbang effect wears off. If an agent runs far enough away, the enemies will not bother to search for the agent. They can be upgraded to improve the duration.

Shock Traps do non-lethal electric damage to targets. They can be thrown or placed on the ground like other grenades. Shock traps can be upgraded to do more damage, and only upgraded shock traps can hurt more than one target.

Remote Mines are mines not activated by the proximity of enemies, but by remote detonation from the agent. Generally an explosive grenade placed as mine works better than a remote mine, and the explosive grenades are cheaper. Remote mines can be upgraded so that more can be carried at once.

First Aid Kits heal the agent. Upgrading the first aid kit increases the amount of health restored, and the number of kits that can be carried.

Epinephrine Spikes inject the agent with epinephrine (adrenaline), increasing melee damage and recoil control of guns. Also increases resistance to damage. These can be upgraded to give longer lasting adrenaline rushes.

Radio Mimics can be used to automatically disable an alarm. They send a radio frequency to the other guards that the agent in question got away. This disables the alarm, but will not deter any guards already pursuing you. Upgrades allow more mimics to be carried.

Sound Generators produce a sound at a remote location, causing near by guards to leave their post and investigate. It might be a bug, but it seems to sometimes backfire and reveal the agent's location instead, sometimes even setting off alarms. When it works, this gadget is useful, but it is a gamble everytime.


Intelligence is a powerful and unique way to learn about the game. Intel is partially backstory, similar to audio logs and diaries in other games, but it is also partially gameplay. Intel may explicitly say what attitude a character prefers, or it may strongly hint at it. Intel can also give you an indication of how trustworthy a character is, which is helpful when trying to decide if you want to work with or against a particular character.

You can also obtain intel on organizations. Like character intel, organization intel is mostly backstory and information to flesh out the storyline. Any organizations you can fight, however, will have some intel revealing common strategies, weapons, and armor. You can use intel to learn if an organization relies on grenades, will try to flank in combat, or will do a headstrong charge. This can be helpful, but it is never vital or required to read intel. Whatever information you can learn intel, you can deduce yourself just by fighting the enemies.

A handy aspect of intel is, if you unlock information on a character or organization, this information will automatically affect dialogue options for you. So you do not need to memorize random facts about the characters or organizations. As soon as you have the intel, Agent Thorton knows the information, and can use this in conversation. If he knows a sufficient amount of intel, he can sometimes choose a special dossier option during dialogue. Othertimes, he will offhandedly mention the knowledge he's obtained.

Intel can be obtained in multiple ways. It can be found on computers, in briefcases, in safes, and other caches in the game world. It can also be bought from the Clearinghouse. Sometimes an ally will e-mail you intel on an upcoming mission. Finally, your conversations with characters and organizations can sometimes reveal intel. If all else, obtaining intel can automatically earn you some perks that will improve damage against enemies and bosses. It is always worth the time and money to obtain intel, but it is up to you if you want to actually read it. You get the benefits regardless if you read it or not.

The intel screen will also show you your current mission list. If you press the cancel button on the mission list, you can view the region list instead, which will let you select a different region. If you are currently on a mission, the intel screen will show you the map (if available) and mission objectives.


E-mail is another source of backstory in Alpha Protocol, and is completely optional. Characters will usually send you e-mails after every mission, sometimes responding to your performance or decisions, or sometimes telling you more information about the plot. Occasionally, Agent Thorton can reply to e-mails. If he is replying to a specific character, treat this is an another dialogue option. It is simply an opportunity to earn favor or anger.

Some e-mails come with attachments that can be downloaded. There are two attachment types: money and dossiers. The former is obvious. Downloading a money attachment adds funds to your account. The latter is also obvious, as it provides more intel on a character or organization.

Throughout the game, Agent Thorton will receive incriminating evidence of political conspiracy and corporate corruption. Agent Thorton has the option to blackmail the corporation with this evidence, earning $15,000 dollars, selling it on the blackmarket for $5,000, or selling it to the press for $1,000. The last option also earns positive reputation with the reporters. The first and second options do not affect any reputations, and do not affect the storyline or ending. The only reason to sell the information on the blackmarket is for personal roleplaying reasons, there is no storyline or gameplay benefit. It is best to use the evidence as blackmail for maximum profit, or to sell it to the press for a better reputation.

Service Record

The Service Record is a character sheet for Agent Thorton. Here, you can view your skill ranks, unlocked perks, and combat statistics. You can view your service record anytime by opening the menu. It is also automatically shown everytime you level up and reach a checkpoint.

Note that Agent Thorton does not have any inherent attributes besides skills and perks. Unlike other RPGs, he does not have a strength, charisma, etc statistic. Instead, these statistics are found on the weapons and armor, or within the skills and perks. The only stats inherent to Agent Thorton are his health and endurance ("shields" in other games).

Skills define your character's abilities. Each skill has a potential maximum of 15 ranks, and each rank costs a certain amount of AP to purchase. The amount of required AP depends on the skill. The maximum rank available depends on the character's level. At level 1, skills can only be maximized to rank 5. All ranks are available at level 14 or higher. Unspecialized skills can only be maximized to rank 10, while specialized skills can be maximized to rank 15.

Perks are unlocked after completing certain storyline or gameplay events. Consider them in-game achievements that offer bonuses. An individual perk usually has a small bonus, such as a 5% discount on buying weapons. These bonuses are additivie, however, so earning enough perks can have dramatic results. Also, since gameplay perks are rewarded for certain actions, many of your perks will improve aspects of the game you enjoy most. A stealthy character will earn perks that benefits stealth, while a gadget using character will earn perks that benefit gadget use.

More information on classes, skills, perks, and statistics can be found in the appendix sections.

Hacking Minigames

The hacking minigames collectively refer to hacking, lockpicking, and electronic bypassing. These three minigames are initiated when hacking computers, unlocking doors and safes, bypassing keypads, and other security measures. The sabotage skill directly improves the efficiency of the hacking minigames, making them easier by extending the time limit.

Hacking opens an interface similar to a word search. Most characters in the word search will constantly change to different letters and numbers, with the exception being the password. The password characters do not change letters, so the goal is to find the string of letters and numbers that does not change. Once found, line up the password with the supplied code. Once both passwords are found and locked, the hacking minigame is completed. On the PC, the codes are controlled with the keyboard (left) and mouse (right), while the left and right analog sticks control the codes on the console. Note that the a scrambler will reset the positions of the passwords every few seconds, so you have to actually work against two time limits. Hacking can be a difficult minigame to master, so make it easier by getting some sabotage skills.

Lockpicking is the easiest of the minigames. The goal is to line up the grooves of the pins with a central line. Once all the pins are in place, the door is unlocked. On easier difficulties, or with sabotage skill training, the minigame will highlight the lockpick when the pin is correctly lined up, making it easy to never fail this minigame.

Bypassing can also be an easy minigame, but on higher difficulties, bypassing becomes the most difficult of the three. Three computer boards will be presented with wires connecting to notches on the bottom. Some of these wires will be connected to a numbered circuit. The goal is to press the notches in numerical order within the time limit. This is as simple as tracing the wires from the circuit to the notch and clicking the correct button. There are a limited number of circuit patterns, too, so you will eventually memorize the correct notch to press just by doing it enough times.

Failing the minigame by letting the time run out, or aborting will cause the alarms to go off. Time is not paused while you are doing the hacking minigames, so enemies can still shoot and kill you while you are hacking and lockpicking. If you incorrectly line up the codes, pins, or notches during the minigame, you will lose time.

The hacking minigames can be skipped by using EMP charges. This requires carrying the EMP charge in your inventory during the mission, so you can only skip a limited number per mission, depending on the number you carry. If you are having trouble hacking computers, I recommend buying EMP charges and saving them for computers, and doing the keypads and lockpicks manually. Note that you need the first rank in sabotage to use EMPs without destroying the electronics.


Combat is straightforward in Alpha Protocol. Players familiar with other action/shooter games will find Alpha Protocol to play mostly the same. One important distinction to made, however, is that guns are not guaranteed to hit an opponent. Even if you have perfect aim, your accuracy is partially dependent on your character's stats and his weapon. For players coming from pure shooter games, this may be a new and frustrating "feature." The best solution is to buy better guns and to improve your character's skills.

Alarms will usually go off when you start a firefight. Most rooms have an alarm box to bypass, if you wish to disable it. This is completely optional, as you will likely set the alarm off in your next fight. It can be advantageous to stop an alarm if you are being swarmed by enemies, because more enemies will spawn when the alarms are active. If you do not want to bother with alarms after every fight, but do not want to be swarmed by enemies, carry some radio mimics with you. This will let you disable the alarm between fights without having to hack the electronics.

Criticals are the passive ability of each weapon. Unlike other shooter games, you are not limited to just shooting your guns. You can time your shots, carefully aim, or charge your criticals for special effects. All criticals will do more damage. Shotgun criticals also knock opponents off their feet. Soldiers using the pistol, SMGs, and shotgun should try to maximize the number of criticals they score. Of course, users of the assault rifle should also try to get as many criticals as possible, but the assault rifle is already innately a powerful weapon and can get by with less criticals.

Active abilities are short duration boosts to your weapon. These can stop time, make every hit a knockdown, or even give you unlimited ammunition. They are on short cooldown, so do not "save them for a rainy day." When they are available, use them, especially if you encounter a large group of enemies. If you are worried about needing them for a boss, most bosses have a talking sequence before the fight. Your cooldowns continue to recharge during the discussion, so simply extend your conversation before fighting to guarantee you will have your special abilities.

Enemies will patrol or guard certain areas of your room. If other enemies become alerted to your presence, they may warn their friends, even if they do not set off the alarms. This can cause enemies from neighboring rooms to join the firefight. If this walkthrough references enemies at certain locations and you do not see them, then you probably already killed them in a previous room.

Surviving combat requires staying behind cover and watching your health. Like other shooters, you have a recharginge pool of shields (endurance) above your health. This is represented by the meter of gray shields. Increasing your skills and armor can increase your total amount of endurance, and lower the recharge time. The red bar below endurance is your health. Health does not automatically recharge, but it is not depleted until you have run out of endurance. If you do lose health, use the first aid kits provided on the walls to heal. These are usually foud in rooms with many enemies, so it is always convenient. If you need additional healing, don't forget to use your first aid gadgets.

About Stealth

Stealth is the harder route to take in the game. It plays similar to other espionage games, with a few minor tweaks. Patrolling guards can both hear and see your character, so you want to minimize their radius of detection by moving silently and out of their field of vision. You can achieve both by always crouching and hiding behind cover. If you are going to move close to a guard, stay behind him. You can reduce the radius of detection by buying better armor, purchasing more ranks of stealth, and earning stealth perks.

After you kill or take down a guard, you will leave his body behind. You cannot move it, but it will disappear after a short time. Before it disappears, other patroling guards can see it and set off alarms. To avoid this situation, go after patroling guards first when possible. The stationary guards are easier to take down after the patroling guards are removed. Sometimes this impossible because a stationary guard will be directly watching a patroling guard. In that situation, you are forced to kill the stationary guard first, and hope you timed it so you can get the patroling guard before he sees you.

Alternatively, you can take down multiple guards at once using your pistol. The pistol is your best friend. As soon as you can, put a silencer on the weapon. This will let you dispose of enemies from around corners or at range, which will make crowded rooms much easier to handle. In situations where guards are grouped together and shooting one would give away your position, use chain shot to dispose of all the guards at once. Always aim for the head, and always let your aim settle (zooms to a red crosshair) so that you get a critical hit.

If you do not want to use the pistol, you have the option to use the assault rifle with subsonic (silent) rounds. These rounds are rarer and not available in the beginning of the game, but they do provide a long distance method of disposing guards. The assault rifle does not have chain shot, however, so shooting one guard in a group will provoke the other guards, and they will probably set off the alarms.

A final alternative to the pistol is relying on your stealth abilities exclusively. The higher ranks of shadow operative give you 12-20 seconds to move around completely undetected. As long as you remain crouching, you can walk into an entire group of guards and perform stealth attacks on all of them. This will not remove your shadow operative effect, so you can move from guard to guard without being detected. It will put them in a state of alert (yellow target display), but the game will not consider you detected.

You can see these target displays using your awareness skill. At lower ranks of stealth, you must manually activate awareness. Once you reach stealth rank 5, however, awareness becomes a default ability that is always passively on. Awareness reveals the location, direction, and alert level of all near by enemies. The direction they are facing can be somewhat misleading if you are not directly facing them, so be sure to rotate the camera to get the proper angle.

Blue targets have not detected you, and are not alerted to potential dangers. They will not sound alarms. Yellow targets have not detected you, but they have seen a strange occurence. Maybe they briefly saw you, or they have seen a fellow guard on the floor. A yellow target may sound the alarms. Red targets have detected you and will open fire. They will usually sound the alarms. (Note, sometimes enemies will be red targets if your allies are fighting them. They may not have personally detected you, so if you remain hidden, they may return to yellow alert level after your allies have left or died. The game may still record you as being detected, even if it was just your allies. Some missions force you to have allies, so don't worry about trying to have a perfect stealth career during those. The game will let it slide during them.)

Lethal vs. Non-Lethal

When you sneak behind opponents, you have the option to take them out or kill them. A non-lethal take down is never required by the game, so you can choose to play using non-lethal attacks or lethal attacks. If you choose to play non-lethally, you can also use tranquilizer bullets with the pistol, or engage in combat with martial arts. Some characters will commend your preference to non-lethal attacks, but this is mostly during the early game. This commendation will earn you, at most, a single point of reputation. More often it's a pat on the back with no gameplay bonus at all, and no effect on the ending. It does not change the storyline if you went the entire game doing exclusively non-lethal attacks.

Important! Civilians and Americans:

The one major exception to the non-lethal vs. lethal debate is civilian and American characters. If you choose to kill civilians (like hotel security) or American agents (like the CIA), you will alter the storyline and the ending. Most characters will disapprove of harming innocents and fellow countrymen. On the other hand, you will impress some characters by showing no preference in who you kill.

Using primarily non-lethal attacks (take downs and tranquilizer pistol bullets) will earn you some perks. You will also earn perks by using the lethal stealth attacks. So no matter your choice, the game will reward you with perks that will make it easier to continue your path of mercy or stealthy death. If you cannot decide between non-lethal and lethal, consider your options:

Non-lethal attacks are harder and limited. You can use stealth take downs, martial arts, tranquilizer bullets, or some gadgets. Tranquilizer bullets are limited, and you may run out during a mission. If you want to play an entire mission undetected, you have to balance your use of tranquilizers and stealth take downs. Martial arts will reveal your position, and may set off alarms. Non-lethal take downs have a longer animation, making it more likely to get caught during them.

Lethal attacks are easier and varied. You can use regular or armor piercing pistol bullets, or the assault rifle with subsonic (silent) rounds. It is next to impossible to run out of regular pistol ammunition, so you will not have to worry about budgeting your ammo. You can also perform a stealth kill using your knife. This animation is faster than the take down, making it less likely that you will be caught.

Lethal and non-lethal are not mutually exclusive. You can definitely play the game using mostly lethal attacks, but switch your pistol's ammunition to tranquilizers when there are Americans or civilians near by. In fact, this is recommended, as it saves your tranquilizer ammo for the occasions when you need it. Sometimes it's best to avoid civilians all-together by simply sneaking around them. The game is slightly buggy, and will sometimes erroneously think a non-lethal take down or tranquilizer bullet was actually a lethal attack. To avoid this bug, avoid attacking any civilians by staying out of their vision, or by using your stealth abilities.

Important! Stealth-Acknowledged Dialogue

Throughout the game, NPCs will sometimes have different dialogue based on your combat actions. If you are a loud, run-and-gun player, NPCs will acknowledge this. If you stick to the shadows and take out enemies silently, NPCs will also acknolwedge this. Most often, NPCs distinguish between a combative character and a stealth character by the number of alarms you set off. Most often, to get the special stealth dialogue, you will need to finish the mission without setting off any alarms, unless they are scripted to be set off. Rarely, you sometimes need to complete the mission using exclusively non-lethal attacks, or even more difficult, without every being detected (awareness setting is always blue or yellow). In the mission details before each mission, I will state which kind of stealth is acknowledged by NPC dialogue (no alarms, no lethal, or no detection). Some missions, such as one in Saudi Arabia, have multiple dialogues based on how stealthy you were, others are different by doing the minimal amount of stealth.

As a final note about stealth, take advantage of a simple gameplay fact: guards do not spawn until you enter their room. If you clear an entire area of guards, feel free to stop crouching and run around. This can be a handy feature to exploit in larger rooms, or outdoor areas. You can save time and explore quicker. Simply re-activate your crouching position when you enter the next room or area.

What are the "good" choices? What are the "evil" choices?

Alpha Protocol does not have a morality meter, unlike other western RPGs. Instead, every action is designed to be a shade of gray, each with its own set of consequences. If you are having a hard time deciding which choice to make, then the game designers did their job. They wanted each choice to be a hard decision that makes you think. If the choice ever does seem clear, take a moment to second guess it. There might be more to the story revealed later, and you do not want to make a rash decision that will permanently block of storyline threads.

What is the best weapon class?

The best weapon depends on your chosen playstyle. In general, the assault rifle is the best weapon for combat characters, as it does the most damage, has the longest range with the best accuracy, and it has good ammo types. The active ability is not the best, but it is more effective against bosses than the shotgun or SMG. If you are a stealth character, the best weapon is hands down the silenced pistol. The special ability for the pistol is essential for some areas of the game if staying undetected is the goal. The pistol also comes with non-lethal tranquilizer darts, making it the best and only long ranged, non-lethal attack.

Is there a benefit to playing non-lethally?

The storyline has minimal acknowledgement of playing non-lethally. Only one mission explicitly mentions it, and it's only in an e-mail. The ending is not changed by using exclusively non-lethal attacks. The biggest difference is using non-lethal attacks on civilians. This does have a larger impact on the story, and it will lower reputation with certain characters, as well as change the ending. Gameplay wise, the game does provide perks for playing non-lethally, making it easier to stick a non-lethal playstyle. This is the same as any other weapon style, however, as the game rewards perks for using the same weapon consistently.

I'm stuck on a boss, what should I do?

An easy to forget feature of this non-linear game is, you are not limited to one region at a time. As soon as you have access to flying around the world, you can tackle the regions in any order you want. If you get stuck in a region, fly to a different one. You can access the world screen by going to the mission select screen and using the cancel/back button to move a screen back. Go to a different region and do some missions, level up, acquire better amor and weapons, and try the boss again. Sometimes a single skill can make all the difference. Sometimes you might get stuck against a boss that can instantly kill you. These just take patience, so you can learn their attack pattern and avoid their lethal attacks. Read the walkthrough for more strategies for each individual boss.

Is stealth or combat better?

Neither. The game will reward both playstyles, and the storyline adapts itself. Entire groups of allies prefer a specific style, but you can be friends with anyone no matter your style. If you play a perfectly stealthy character, a semi-stealthy, or full combat character, you will still find an enjoyable game. People looking for a challenge will find the perfectly stealthy route to be the hardest, but that does not make it inherently better.


Saving the world isn't easy, and Agent Thorton certainly faces his share of hurdles and enemies. This walkthrough is organized by region to make browsing easier. Use the table of contents to select the region or mission. The game is non-linear, so after a certain point, Agent Thorton can travel to any region in any order. The listed order in this walkthrough is arbitrary--it is not listed by difficulty, importance, or any other factor. Truly feel free to do them in any order.

Not only can Agent Thorton do the regions in any order he likes, he does not need to stay in a region to the end. Feel free to do part of a region, then fly across the world and do some missions elsewhere. If you are having trouble on a boss, go do some missions elsewhere and earn some levels to make the boss easier. The game only requires that you complete all the regions before you do the final mission, and it requires that you do the Middle East first.

This walkthrough will attempt to limit the spoilers. The plot of each mission will be hidden a spoiler tag at the beginning of each mission section. The rest of the guide will limit spoilers, but beware of accidental spoilers. Reading the list of mission titles, boss/enemy names, or locations may give away some plot details. These will be minor details, but if you are worried about spoilers, be careful about reading too far ahead.

SPOILER! Highlight to View

Important plot details will be revealed in these boxes. If you want to wait and experience the plot for yourself, skip these boxes and read the mission instructions instead.

Mission Details:

Dossiers, items, weapons, armor, and the amount of money found on the mission will be shown in these boxes. Take note that items are randomly generated after the first region. There will also be a note warning if there are civilians or Americans in the mission that you should use non-lethal attacks on. Finally, I will note if the storyline acknowledges your stealth level. This last part is just for fun. Characters will almost never outright reward you for being stealthy, but their dialogue or e-mails might be slightly different. Each mission has a different threshold of stealth you must fulfill for the dialogue to be different. As long as you maintain that amount of stealth minimally, you will get the special dialogue.

No Alarms: The most common treshold. The dialogue sill be different if you set off no alarms during the mission. Scripted alarms (such as the one during the tutorial) do not count against this. No Lethal: Some handlers will optionally acknowledge that you did the entire mission without killing anyone, civilian or otherwise. You can still use non-lethal attacks, like martial arts, tranquilizers, and some gadgets. No Detection: The most difficult level. You must remain completely undetected by the guards, meaning, their awareness is strictly blue or yellow level. A "no detection" handler also automatically assumes "no alarms." Not Acknowledged: This mission does not acknowledge stealth, so you can set off alarms or be detected without worry.

If you are new to the game, or new to RPGs and action games, I strongly suggest that you skim the Game Basics, Appendix I: Classes, and Appendix II: Skills sections before continuing. If you are familiar with RPG traditions, then most of the information in these sections will be common sense. When you are ready, create your character, watch the opening video, and begin your first mission, escaping the Graybox!

As a final note: if you are focusing on combat, you may find parts of this guide are tailored to stealth characters. To be honest, stealth is more complicated than simply running in and shooting, so it needs additional instructions. That said, there is still valuable information for you. You will know where guards are, and how many are present, which can help when trying to figure out where those stray bullets are coming from. Be warned that additional guards can spawn when the alarms are going off, so there may be more in other places not described. The additional spawns are strictly random, but you can avoid them by deactivating the alarms with gadgets or hacking the alarm boxes.

Mission Details:
  • Dossiers: Alpha Protocol (x2), Mina, Westridge
  • Items: Pistol, Tranquilizer Ammo
  • Money: $2500
  • Perks: News Conscious, Attitude Perk (Suave, Aggressive, or Professional)
  • Civilians: None
  • Stealth: No Alarms (scripted alarm is ignored)
SPOILER! Highlight to View

The opening video shows an airplane being shot down by a high-tech missile. The camera zooms back to reveal a mysterious man dressed in a business suit is watching the video. Behind him, a man named Agent Thorton enters the room. The mysterious man taunts Agent Thorton. As the agent sits down, the mysterious man points out that they are sitting in the same facility where Alpha Protocol began.

The story then shifts to three months earlier, where Agent Thorton is shown waking up in a medical facility. He is awoken by a phone call on his PDA. The caller is Mina Tang, a fellow agent at Alpha Protocol. She warns that Thorton needs to escape from the medical facility, and offers advice on how to escape. During his escape, Thoton is taunted and harrassed by a guy named Westridge. Thorton finally manages to escape the medical facility, but he is captured in an interrogation room. Westridge finally reveals to Thorton that he just completed the normal "initiation hazing" that all new agents undergo.

Following his interrogation, Agent Thorton explored the rest of the facility. He learns on TV about a terrorist leader named Shaheed and his organization, Al-Samad. They are threatening to use more missiles against America.

Escaping the Medical Facility

When you first wake up, the game will give you a short tutorial on how to move your character and the camera. Once it asks you to pick up the PDA, you will find it on the counter near your bed. It is in the corner to the right of the door. The PDA will have a faded circle symbol above it, signalling that you can interact with it. Answer the PDA phone call with whichever attitude you like, it does not affect any relationships.

Mina will ask you to escape from the medical facility, and will offer advice. Choosing "ambush" will set off the alarms immediately, while "distraction" will let you sneak out. "Ignore" and "improvise" will do nothing. If you choose these options, you will need to use the fire extinguisher next to the door to break out. This will set off the alarms. If the alarms are set off, a guard will run into the medical room and attack you. If you did not set off the alarms, you can sneak out and find the guard in the hallway. You will automatically earn a dossier on Mina after your conversation.

Leave the hallway using the door on the farside. The elevator will not work. In the next room, you will do a minigame tutorial to shut off the alarm. Review the Game Basics if you need help with the minigame. If you chose "distraction" earlier, the alarms will automatically trigger by entering this room. Once the alarms are disabled, the next door will unlock.