Okay, so the majority of you right now have got to be thinking somewhat the same thing. "What the (bleeep) just happened? Why did Desmond kill Lucy? What was Juno talking about? And what went on during the credits?"
I myself have no idea either, but putting together the puzzle pieces I have, I've come up with several ideas as to what the answers are. So for the first question, here is pretty much what we know for right now: Desmond was using the Animus 2.0 in Brotherhood for one reason, which was to find out where the Apple of Eden was.
After killing Cesare Borgia, it goes on to a scene where Ezio and Leonardo are debating over what they should do with the apple. Ezio decides that it needs to be hidden, so of course he stores it away deep inside the colloseum. Once this discovery is made, the power goes out, leaving you unable to go back inside the Animus in order to see exactly where it is in the colliseum, and how to get there.
Anyways, so you and the rest of the team go there to search for it. Due to the bleeding effect, Desmond sees ghostly images of Ezio, helping you lead the way as to where to go and what to do. You will also encounter Juno, another one of "Those Who Came Before". Now, do you remember the first Assassin's Creed? Where Vidic answers your question with, "It is a gift. A gift from those who came before." That definitely has to say something about how the Templars and "Those Who Came Before" must be connected.
Eventually, you make your way to the main room, with all of these strange hyroglyphs, a large platform holding the Piece of Eden, and strange columns you must climb in order to reach it. Once gaining access to the platform, a staircase pops up, leading you to your goal. However, this results in Desmond interacting with the Apple, and this is when everything goes down the drain. First, time seems to either stop, or freeze. Desmond tries to fight it, but something is controlling him, being the Apple of Eden.
It leads to you involuntarily stabbing Lucy. I do not use 'killing' because it is not confirmed if she indeed has died or not. Following this, Desmond collapses to the ground, evidently in a moment of shock. But before we move onto the credits, let me give you my insight on the other questions you possibly might have. Let us continue with, "Why did Desmond stab Lucy?"
Quite frankly, he didn't. I'm not exactly sure as to how this small part all falls into place, but from what I understand, Juno or one of her kind/people/slaves programmed something into the Apple to force Desmond to kill Lucy, so that they couldn't have a 'relationship'. Well, a 'serious' relationship anyways, if you know what I mean.
To continue on this point, in my Collector's Guide, it mentions this too. It wants Desmond and Eve to mate (unless I totally misunderstood it) so that a new race could be born. In other words, so that the world could be cleansed, and could start anew so that the "Ones Who Came Before" could rule once more over humanity.
Therefore, seeing how Lucy could intervene with this, the magical power stored in the Apple forces him to stab her. But if you look closely as to where Lucy is stabbed, it is in the side, in the bladder area by the looks of it. In my opinion, this is not really the most crucial area, which leads to me believing that Ubisoft wants you to think she dies, but she merely gets critically injured.
This should also have answered as to what Juno was talking about. To recap, a VERY long time ago she used a Piece of Eden to look into the future. She saw Desmond being the 'one', or of some importance, and placed an ability in the Apple that would control him. She must have also stored part of herself into it as well, so that she could ensure it all went according to her plan. This results in Desmond stabbing his most trusted friend.
The last question, "What happened in the credits?" I believe that Desmond went into a state of shock, and to help with it, threw him back into the Animus. But who put him back in? Who was that voice? I think it was Desmond's father, or maybe Subject 16. "But how in the world could it be Subject 16?" Simple. Subject 16 faked his death (although really did scrawl all those things in blood on the walls). If you go back to Assassin's Creed II, you use Eagle Vision in order to access the code on the locked door. Who entered that code? Sure, one of Abstergo's employees could have.
Or, it could have been Subject 16 entering it in his bloody fingers, indicating as to why it is red, just like the things in blood in the room. He was leaving you messages not only on the walls in real life when he started going insane, but he also hacked into the Animus so that he could leave you messages there incase the blood messages got wiped off beyond recognition. Another thing that leads to this is the achievement written in Morse code. It can be translated to 'I AM ALIVE'.
I also must say, that I'm pretty sure "Those Who Came Before" are the bad guys. Why else would they give the TEMPLARS a gift, the Animus? This is kind of contradictory as to the reason why Juno wants Desmond to kill Lucy, but here we go. Juno only wants Desmond to kill Lucy because Lucy is helping him find the other Pieces of Eden. Juno doesn't want her to help him, and therefore uses the power to control Desmond (similar as to how the Apple, when playing as Ezio, can cause Borgia guards to attack one another) in order to try and kill Lucy. Whether this was successful or not, we are unsure.
So these are my views on this crazy cliffhangar. So many things going on at once, so many things to keep track of! But I'm not known for being correct. In fact, I'm sure that this is far from being right. Which is why I would like to see what you guys have to say on my theories, but also about any theories or possible answers you would like to share.
Thanks for reading, and I look forward to reading yours in return.
