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You have a menu with different upgrade options at the bottom of the screen, and each time you collect one capsule it will start browsing to the right on that menu. For example, your first capsule will highlight "Speed Up", and then the second capsule will highlight "Missile", and then it will keep browsing right like that. If you collect another capsule when "?" is highlighted, it will simply browse back to "Speed Up" again. You choose the highlighted upgrade by pressing B.
"Speed Up" doubles the speed of your ship, and you can keep upgrading the speed for as long as you want, although I would recommend to only use maybe 3 Speed Ups, since anything more than that might make the ship too fast and hard to control.
"Missile" drops missiles on targets below you while you are shooting, and the missiles will keep moving after they are dropped on a surface.
"Double" shoots additional bullets diagonally upward, which is very useful on stages where a lot of enemies run around above you. This attack is disabled if you choose "Laser".
"Laser" is a forward laser attack that replaces your original shots, and it is very powerful particularly on strong single targets (i.e. bosses etc), although it is fairly useful in general. This attack is disabled if you choose "Double".
"Option" gives you a robot that will mimic your shots, and you can get 2 robots in total.
"?" gives you a protective shield that makes you invincible to a few attacks. It will start out blue, and then turn red when it is almost worn out. It is wise to keep this powerup highlighted when you have nothing else to pick, so that you can immediately choose another "?" when the old one stops working.
All powerups disappear if you die, although sometimes you might start with "Speed Up" highlighted.
Also, one tip - do not hold down the A button at the beginning of the first stage; you can kill the first incoming rows of enemies much faster if you keep pressing the button manually instead.