At the end, Desmond dies. I was under the assumption with all of this hype and talk, that Assassin's Creed 3 will be the final installment because the whole series was based on Dec. 21, 2012. And in the third game, it happens. Desmond dies and basically sets free this First Civilization person, Juno, who wants revenge on humanity, in order to save the Earth on the 21st from a Solar Flare. It was either that, or let the Earth be scorched, killing billions of people, and only Desmond and a few live and life basically restarts from the Bible ages.
But Desmond decides no, lets out Juno, he dies, she starts to walk the earth in order to basically get revenge on humanity.
There were so many unanswered questions and it was a poor ending. Now instead of going off of like real world events like 2012, they're basically making their own story out of it now. Which sucks. And the ending of the game contradicts what happens in Brotherhood. In Brotherhood one of the First Civ people, Minerva, takes control of Desmond, and kills Lucy because she's a Templar. But in AC3, Desmond says that he wanted to kill her. So really, everything that was set up from AC1 to Revelations was thrown out the window with no real ending, and instead have this like somewhat new ending pushed down our throats. Which basically means, yeah, there's going to be an Assassin's Creed 4 and the Templars and Assassin's might team up to destroy Juno, which means that the Assassin's and Templars were sort of after the same thing.
Which is more confusing because in AC3 when you're playing as Conner, your dad is a Templar and he even says they want the same thing. But in previous AC games, The Templars (Abstergo) wanted to put a satellite into space to control people. So the writers actually changed the entire fucking story all together.