Please note that these theories are all hypothesized by fans of the series and in no way does Showtime confirm or endorse them.
1. Brody is still pulling off a master plan hatched by Nazir.
Nazir’s successors no doubt have a longer game in mind, and they already know that Brody gives into emotional manipulation. Plus, given his relationship with Carrie, he will still have access to her contacts and talents.
2. Saul is the mole.
We know that there is definitely a mole somewhere in the CIA, and Saul was seriously the ONE guy not to attend the memorial? He’s also had numerous problems with Estes in the past and, given that Saul is now heir apparent to the CIA leadership, he had plenty of incentive as well.
3. Issa Nazir was Brody’s son.
We know that Brody loved Issa as though he was his own son, but what if Issa actually WAS his son? Brody was held captive in Iraq for almost a decade and his relative ease of access to Nazir and his compound could have led to some… not exactly ethical liaisons.
4. Carrie’s relationship with Brody is all in her head.
He has always been more removed, and Carrie has a history of mental instability. What if her bipolar disorder goes further than that? What if she became so attached to Brody over their few fleeting times together that she exaggerated their connection and built a whole world around it?
5. Peter Quinn is an agent of Abu Nazir.
Quinn made it perfectly clear that he takes out bad guys and that Estes was one of them. We don’t actually know much about his background, his ambitions, or exactly why he was so opposed to Estes. Can we really trust someone so intimately involved with the agency that we know so little about?
6. Dana is part of Nazir and Brody’s terror plot.
Dana has always been trying to get closer with her dad, and perhaps the only way she thought she could get close to him was to help him execute Nazir’s plot. That would explain why she cozied up with Finn, despite their somewhat rocky relationship: to get closer to the VP. Now, with the Waldens out of the picture, why wouldn’t the media begin to scrutinize her own doings? There was that nasty car accident thing, after all.
7. Season two was a dream.
At the end of season one Carrie undergoes electroshock therapy. She begins the second season in a relatively happy state, seemingly able to finally pursue a relationship with Brody. But as the season goes on, things slowly (and then quickly) unravel—as she begins to regain consciousness. So what if Homeland went in a surreal direction and season two was all a dream she had while unconscious?