What's driving Juno? When young Connor sees a vision of her, she says "What once was shall be again", implying that she wants to restore the First Civilization to its former glory before the solar flare struck. She may know a way to bring her people back, or maybe she will be the lone survivor; an all-powerful dictator using an army of human slaves to do her bidding.
Or maybe it's simpler than that. Maybe she just wants revenge. A rebellion of human slaves (including Adam and Eve from The Truth) destroyed much of the First Civilization's influence on Earth, and she may see that as the catalyst for their inability to stop the solar flare and ensuing destruction. If this is the case, she's held a grudge for over thousands of years. Her husband, Aita, was killed as a result of the rebellion, so she may be driven by grief as well.
Whatever her motivation, she's now the official big bad of the Assassin's Creed series. Whoever the new hero is, he'll have quite a job on his hands. But he may have guidance, from Desmond. Yes, he died, but Subject 16 was dead too, and he had a starring role in Assassin's Creed: Revelations. Either the Animus, or the technology that allows Juno, Minerva, and Jupiter - or at least their minds - to live on thousands of years after their death, could be used to bring Desmond 'back', perhaps to guide and share his knowledge with the new protagonist.
However the Assassins decide to stop Juno, it will involve going back in time. But how far? An optional conversation with Shaun in the temple reveals that he wants to try and turn back the dial on the Animus further than they ever have before: back to the time of the First Civilization. Desmond says he's up for it, but Shaun wonders whether the memories will be stable. Altair was, after all, only a thousand years ago, and he's talking about going back by almost 80,000.
BACK TO THE FUTURE
So could the next game be set in one of their cities? Could the ancestor whose memories we inhabit be the one who started the human revolution? It's a cool idea, but we're not sure. One of the things that defines Assassin's Creed is the historical setting. Ubisoft Montreal are masters of recreating specific time periods, digging through the history books to make it as authentic as possible. If they went back to the First Civilization, they'd have to create a city and culture from scratch. They could do it, but it wouldn't be in line with the rest of the series.
If they stick with reality, which is more than likely, there are still a lot of time periods to explore. Feudal Japan, Sumer, the First World War, Victorian England, the Russian Empire, Ancient Greece. The list is as long as human history, and if they can make the American Revolution work, they can make anything work. As for the present day, we may see the Templars and Assassins finally joining forces to crush Juno's plans, but it won't be an easy alliance. William Miles tells Desmond in another optional conversation that they've considered uniting in the past, but that they'd be too paranoid about each other to make it an effective partnership.
Whatever happens, we will see more of Assassin's Creed. If they continue their theme of releasing one a year, it may be sooner than we think. We're fully expecting another Brotherhood-style 'half sequel' before the next game, but we wonder how they'll deal with the fact that Desmond is gone. Connor is relatively young by the end of Assassin's Creed 3, so there are still a lot of stories left to tell there. Maybe it'll be set entirely in the 1700s, or we'll see a digital construct of Desmond inside the Animus like Subject 16 in Revelations.
There's still a lot we don't understand. Like how exactly Juno was able to stop the solar flare, and why she didn't use that power to save her own people. Minerva's allegiances are unclear: is she on humanity's side? In Brotherhood we assumed Desmond killed Lucy under Juno's influence, but in Assassin's Creed 3 he says he wanted to do it. But questions are always more fascinating than answers, and we're glad there are still some mysteries left to be solved.
Assassin's Creed 4 will be a next-gen title, and we can't wait to see what they do with it. Expect a direct continuation of the events set up by Desmond's sacrifice, a new hero, and a lovingly recreated historical setting to explore - all powered by new hardware.