I don't understand the ending!

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.

Solution 1:

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.

Solution 2:

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.

Solution 3:

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).