Desmond has been through quite a bit. He lived the life of Altaïr and found out about the Templars and the golden apples. He then lived as Ezio who fought to avenge his family, but learned of the greater battle for the world. He gained control of Apple of Eden, used it to avoid the Templars, and then hid it beneath the Colosseum in Rome. He then learned of a temple that can save humanity in New England. He is one man that has experienced two other lives, and now must experience a third. He must see how Connor (or Ratonhnhaké:ton) lived and fought in order to find the key to access the one thing that can save humanity. And from this point onward I will talk about the story, and only the story of Assassin's Creed III. There will be some spoilers to the game, but the spoilers will more focus on Desmond's part of the game and not really Connors. Not that I can really spoil how the American Revolution ended. Nonetheless, you have been warned.
Assassin's Creed III starts with Desmond, Rebecca, Shaun, and William (Desmond's Dad) finding the cave opening on old Mohawk land. They enter and find the temple of the First Civilization along with Juno. She seems helpful enough, and wants the world saved. She really does not like humans though, and I find it odd she would help us. But for now the enemy of my enemy is my friend. And when your enemy is a world destroying event it becomes pretty easy to put aside petty grudges. Soon Desmond is back in the Animus, this time as Haytham Kenway in England. Wait, I thought this was about Connor? Well hold on, I am getting to that. After some sections of Haytham climbing, killing, and the like you find out that Haytham is not even an Assassin, but a Templar. Interesting given that his son, Connor, turns Assassin to kill the man, along with Charles Lee for the murder of his mother. And so we move forward. Desmond lives through Connor's life with brief interruptions to secure power sources for the temple, and save William for Abstergo HQ. There is not much to say on the story of Connor though. He builds a nice community, helps the Patriots until Washington tries to wipe out his people, and gets his revenge. Overall the character was pretty one sided and not as interesting as Desmond's other lives. Connor never grew out of his need for revenge like Ezio did. He never really looked for the greater good in the main story. Sure side missions showed he cared for his community, but considering that those are optional, their is no promise that the player ever saw that side of him.
The story for Desmond is much more interesting. He is dealing with Juno who wants nothing more then for him to save humanity. But what for? She states how primitive apes destroyed all they held dear. How they are nothing compared to the First Civilization. Why save them? Why put forth the effort? Once you find the key and open the way you find out, mostly thanks to Minerva showing up again. The ghosts of the First Civilization you have encountered through the series are not just ghosts, they are the actual people stored in a digital format. Desmond is given two options. Minerva could allow the oncoming catastrophe to occur and then rebuild civilization. This would make Desmond a powerful leader, who will be worshiped as a god after death. People would eventually kill in his name though, and the whole conflict would start over again. The second, Juno's choice, is use the device to save the world, and release her on it. Desmond chooses to save the world, and deal with Juno after. He activates the device. The last thing we see is reports of massive seismic activity quickly turning back to normal. Then Juno tells a possibly dead Desmond that his work is done, and her work may begin.
So our main character may be dead? But after the credits you are returned to Connor and cannot leave the animus as you could during the whole game. Were you set back in the animus to save your life as they did in Assassin's Creed II: Revelations? Or has William entered the machine? I like were they are going with this, moving the greater pearl from the Templars to a First Civilization being. They are going to have to fight on a whole different level now. Will we see Abstergo and the Assassin's work together to solve this problem? Or will they continue to fight between each other to Juno's benefit? To be honest had the story in the present not been a part of the game, if the story had just involved Connor, I would not have gone back to this game. But I want to see where this is going, I want to see it through.