Just you wait and see, it's going to be the freaking Council again.
Think about it: No matter what you did, we either have the same three morons from the first game, or a just-as-moronic, purely human Council.
All this time, they think that Shepard's just delusional, with all his talk of 'Reapers coming to destroy us', and his alliance with Cerberus. So, when Shepard starts taking drastic steps to fight the Reapers, the Council sends someone (possibly another Spectre) to bring you in so that you can't cause any more trouble.
Somehow, they succeed/Shepard gives up, but his squadmates manage to avoid capture somehow, and start planning an ultra-epic prison break where we get to play as our favourite squadmember, and assign people to certain roles like in the suicide mission(e.g. Kasumi/Thane sneak in to rescue Shepard, Grunt/Zaeed distract guards, Tali hacks stuff, etc.). This culminates in a massive escape from the Citadel, where we then go off to save the galaxy, while the Council brands us threats to galactic security, therefore making our job that much more difficult.
I would love this if it happened, but I'm just a sucker for stories where the hero is thought to be the villain and vice versa.