The second season finale of "Homeland" (entitled "The Choice") focused on the ongoing relationship between Carrie and Brody. They both know that Carrie can't work at the CIA and be with Brody, and so she needs to make a choice.
Unbeknownst to the two lovers, the CIA has ordered Quinn to kill Brody now that Abu Nazir is dead. While Carrie and Brody consider their future at a romantic cabin, Quinn is across the lake from them, watching their every move with his sniper scope.
But when Quinn gets a chance to shoot Brody during his morning prayers, he doesn't pull the trigger. His reasons for not doing so are revealed later on when Quinn goes to visit Estes, who gave the order to kill.
Quinn knows that Carrie will be devastated and spin into a depressed state if Brody is murdered. And now that Walden's dead, Brody isn't a political threat. Quinn argues that Estes only wants Brody dead for personal reasons at this point, and that those reasons will cause untold amounts of pain in the life of one of their best agents. Quinn says that if anything happens to Brody, he will return to see Estes and murder him.
Estes goes to Saul, who has been imprisoned for three days, and releases him. Saul doesn't understand why Estes has changed his tune, but he is relieved that Brody isn't dead.
Later, Brody finds Mike Faber at a bar and buys him a beer. Brody reveals that he and Jess are over, and lets Mike know that he would be OK with him getting together with Jess and taking care of the kids. Brody then heads to his home and finds Dana is the only one there. Dana confronts her father about the terrorist plot he almost carried out.
Saul offers Carrie a new position in the wake of Abu Nazir's death. She would become the youngest station chief in the history of the agency, but she is not certain she wants the job. Saul says that if Carrie picks Brody over the agency, she'll be the dumbest and smartest person he's ever known.
Saul then leaves Carrie's side to go preside over the burial at sea that has been planned for Abu Nazir, while Carrie heads to Walden's funeral to support Brody. Despite Saul's protestations, Carrie finds Brody at the ceremony and says that she wants to be with him. Brody looks out the window and notices that someone has moved his car. Just then, a bomb in the car goes off, badly damaging the CIA building where Estes is presiding over Walden's funeral. Carrie wakes up after the explosion and pulls a gun on Brody, believing that he was behind the car bomb.
Brody tells Carrie that he had nothing to do with this, and that it's more likely that Nazir planned the attack. Carrie comes around to Brody's side and tells Brody they need to get out now, because no one else will believe he is innocent.
Saul is told that Carrie and Brody have been presumed dead, but that the bomb was likely placed in Brody's car. Carrie and Brody head toward Canada and plan to use fake passports to get into international waters. As the episode draws to a close, the suicide bomber tape Brody made in Season 1 before donning his vest is played on TV.
At the border, Carrie decides not to cross with Brody: She wants to stay behind and clear his name. In a tear-jerking scene, Brody tells her that what they had was real love, and they embrace. Brody walks off into the woods, leaving Carrie alone.
Saul, now the highest ranking officer at the CIA, presides over the investigation into the attack. As he surveys a room filled with bodies, Carrie returns, and he smiles.