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I just finished AC Brotherhood. Not with the full sync though. Here is what I don't understand (with spoiler tag markup):

At the end of the story when Desmond pickup the apple he kills Lucy! Why? The alien that was controlling Desmond with the apple gave some vague explanation, but I did not understand it.

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For someone who did not play the game, it is juste "what the heck!" – Wok Jun 15 '11 at 15:53
@wok: What? Don't understand you.. – Sisir Jun 15 '11 at 15:59
Also, are you certain that Desmond actually kills Lucy or did he simply stab her? I guess we won't find out until the next game in the series comes out. – Crag Jun 15 '11 at 16:40
Not sure.. But desmond stabbed her and she was bleeding badly. – Sisir Jun 15 '11 at 16:59
Your question made me desire to play this game. :) – Wok Jun 15 '11 at 17:23
up vote 4 down vote accepted

I would advise you to listen to the credits after the game has finished. And also to play the additional memories know as : Assassin's Creed Brotherhood - The Da Vinci Disappearance DLC

The message of the alien seems to be intentionally cryptic. In the credits you can understand that Desmond's reality seems to be another simulation as technicians are talking about Desmond going to shock.

In the DLC :

Same technicians will clearly states that they acquired the wanted knowledge from Desmond who has gone into a coma.

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So our playing as Ezio is a Matrix within a Matrix? Ooooooh.... – Alex Jun 16 '11 at 7:59
I'd say probability raises fast! But I wait for AC:Revelations. – M'vy Jun 16 '11 at 8:00

Lucy is actually a double-agent. She intended to betray Desmond and his "team" and to take the apple back to Abstergo. Juno was aware of this, so she had Desmond resolve the problem.

This is all revealed in DLC for Revelations.

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The end speech is designed to be cryptic, but the gist of it follows.

The gist of Juno's (The glowing character who makes Desmond stab lucy) speech
(You can watch a good video of it here, starting around 4:50.)
is that to save the world Desmond has to awaken his "6th sense". To do this, he has to destroy his psyche (by killing lucy) and rebuild it (the black room levels in Assassin's Creed: Revelations).

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Any idea when next version coming? Can't wait to play!! – Sisir Aug 18 '11 at 7:58

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