Okay, so Desmond's dead, Juno's free, and I assume the Abstergo launch of the satellite will be succesfull. This basically means there's a new First Civilization-Human war. Juno couldn't have chosen a more opportune moment to come back. She knows exactly how the PoE work, and she can now easily control most of the human population, as her personal, docile workforce. The Templars AND the Assassins obviously don't like this, so this might mean they could team up for now, if the Templars don't decide to join Juno. There's a difference to keeping peace through control, and outright slavery. Now, they need to find a way to defeat Juno. This wouldn't be Assassin's Creed if the Animus weren't involved, but Minerva and Jupiter obviously didn't know Juno was still alive at the end of ACIII. So they can't help, even if you go into the past, and search for the vaults. The only plausible way I can see this going is that they need to find a new Piece of Eden, to counter the Apple in the satellite. I can't see the Assassins destroying the satellite, because it's IN SPACE, and Juno would have control over military bases. I suppose, her being a member of the First Civilization, that she's far more powerfull than a human, at least physically. Finishing her head on will thus be an incredibly hard task.
What I would like to see, is for the new Assassin's Creed to go to the Netherlands during the Eighty Years war, fight the Templars, and what not, and ultimately finding a vault in a recently created polder. TWCB would have made a vault under water, where humans couldn't travel in the war between TWCB and the humans. They hid one of their most powerful PoE there, one that could overrule the others. But now that vault is made accessible, and the past Dutch assassin would retrieve it. Later in the story, he knows it's too powerful, and places it back. Now the modern day assassins can find it and take the battle to Juno.
What do you think of this? It's of course pure speculation, but I think it would be an awesome plot.