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Now I'm not sure if this glitch has been discovered, but I just discovered it a little while ago. Unfortunately, it has no benefits (bear with me, it is still an interesting glitch).
Near the end of the first memory block, during the seige, you need to cut a lever to trigger the log trap that ends the chapter. When doing this, I had swung my sword to the right of this lever, and immediately glitched through the wall, falling directly behind the horde of Templars outside of the gates. I moved toward them and my indicator immediately started flashing red, however the Templars made no move to stop me as I moved through their ranks to the front where Robert himself sat upon his horse. I selected my hidden blade, and surprisingly enough, I was given the "Assassinate" prompt. I pressed 'X' and sure enough, Robert was stabbed and taken off of his horse and layed on the ground by Altair,
My Synchronization bar immediately turned red (the way it turns after you perform an assassination on a mission) and the guards began to shout, "Get him!" and other such lines, but still made no motion to stop me. I proceeded to kill them all through assassinations, sword attacks, and throwing knives, and even when attacked, they would not fight back. I eventually killed them all, however they started to respawn.
The problem was, I was unable to reenter the castle because the gate was down, thus it was impossible to return to the area where you activate the log trap (believe me, I tried). I decided I would leave the city and see what happened. On the way out, I was chased by the city guards, who seemed to recognize the fact that I had assassinated Robert. I escaped and entered the Kingdom, where I scaled the first viewpoint, but found myself unable to synchronize. I returned to Masyaf, and after receiving a very odd and moving camera angle, assumably moving from the Templar horde's location, made my way back through the city, being chased once again by the guards, until I reached the castle.
I quickly dispatched the guards that followed me and then observed my surroundings. The Templars still made no attempt to harm me, but my indicator was flashing red again. Robert and his horse were both missing. Also, the castle gate was open, much to my enjoyment. So I strode back into the castle, reclimbed the tower, performed a leap of faith, noticed both my partners had since left, made my way to the ambush spot, and triggered the log trap, ending the first level normally, with Robert in the cutscene and everything.
There you have it. The glitch is essentially useless, as killing Robert does not accomplish anything, but it was interesting to find and experiment with.
In MGS3, it takes place in the past, and you battle a guy who's alive in the future. You can knife him to death which isn't supposed to happen since he's supposed to be alive in the future, so it's a paradox. Quite simple really.
Won't Change This Sig Until Jack Thompson Is Brutally Beaten To Death By Kids "Under the Influence of Violent Video Games."
I haven't tried it again yet, however I intend to as soon as I get the chance. Unfortunately, I do not have a capture device to get a video of it. When I try it again, I'll be sure not to miss my chance at the crossbow! :P