CIA officer Carrie Mathison, who secretly suffers from bipolar disorder, is told by an asset in Iraq that a prisoner of war has been turned by al-Qaeda. Ten months later, Carrie is called by her boss at Langley, David Estes, for an emergency briefing. She finds out that a U.S. Marine sergeant named Nicholas Brody has been rescued from a terrorist compound, after having been missing for several years. Carrie believes that Brody is the traitor her asset was talking about, despite the fact that everyone else is convinced he’s a war hero.
Carrie installs audio and video surveillance at Brody’s apartment to confirm her suspicions. She watches him as he struggles to reconnect with his wife and children. She even discovers that his wife is cheating on him with his best friend. However, she doesn’t find anything to fuel her beliefs; thus, she is forced to shut down the surveillance by her mentor, Saul Berenson.
In her efforts to become closer to the asset, Carrie starts flirting with him. This escalade quickly and an affair blooms. Later, Brody finds out about his wife’s extramarital activities with his friend; soon after, he decides to go with Carrie to her family’s cabin. While there, Brody grows untrusting of Carrie’s intentions and forces her to admit her suspicions. In exchange, he admits he converted to Islam and became close to Abu Nazir, the terrorist leader who held him captive all those years. However, he denies that he’s planning to betray his country. That’s when Saul calls Carrie to let her know that the traitor they’ve been looking for all along is apparently Brody’s partner, Tom Walker, who was also imprisoned by Abu Nazir.
Later, the Vice President recruits Brody to run for Congress. In a riveting twist, Brody secretly contacts Abu Nazir, confirming he is truly a spy for al-Qaeda. Meanwhile, Carrie still has doubts about Brody’s innocence and keeps calling him in the hope that she will get some answers. Brody reports her to the CIA and reveals that she was spying on him, removing her from duty. Shortly after, everyone is convinced that Tom is planning a sniper attack, but Carrie is sure that Brody has something bigger in mind. She tries to tell his family, but nobody believes her.
In a final turning point, Brody is shown wearing a suicide vest to a big political event, planning to kill himself and blow up some major political leaders at the same time. All the while, his daughter Dana suspects he’s hiding something and calls her dad begging him not to do anything he might regret. Her words get through to him and Brody calls the whole thing off. He tells Abu Nazir he wasn’t able to comply with his mentor’s demands due to a malfunction in the vest. Untrustingly, Abu Nazir orders him to neutralize Tom in order to prove his allegiance. Brody conceives and reluctantly kills his buddy.
The first season also deals with Carrie’s deteriorating mental state. Her relationship with Brody and growing suspicions have a negative impact on her psychological issues, and her loved ones soon decide to commit her to a facility. The season ends with Carrie deciding to undergo electroshock therapy to treat her bipolar disorder. Right before she does, she remembers something that proves Brody’s connection to Abu Nazir; unfortunately, she later forgets the incriminating detail because of the controversial treatment.
In season two, Brody starts working for the good guys. During a CIA operation in Beirut, Saul discovers a video in which Brody’s confesses his deadly intentions, recorded right before he was supposed to blow himself up. Saul, Carrie and analyst Peter Quinn work together to turn Brody into a double agent. Brody agrees to this arrangement mainly because of Carrie, with whom he is romantically involved again. However, his relationship with his family gets worse.
Brody is on a fast path to becoming a Congressman, while working as a double agent for the CIA at the same time. Meanwhile, Abu Nazir comes to the U.S. and becomes suspicious of Brody’s allegiance. He kidnaps Carrie and blackmails Brody into finally killing the Vice President. Brody faces a moral dilemma, but accepts the terms of the deal. He goes to the VP’s office and gives Abu Nazir the serial number of the politician’s pacemaker, so the terrorist could induce a heart attack. After the VP dies, Carrie escapes from captivity. Also, the CIA manages to track down and kill Abu Nazir.
Later, during the Vice President’s memorial service at Langley, Brody and Carrie celebrate the fact that they finally got rid of Abu Nazir. Suddenly, an explosion occurs, killing a large number of CIA officers. Carrie suspects that Brody is somehow involved, especially since the bomb was placed in his car. However, Brody convinces her that he’s being framed. Surprisingly enough, this turns out to be true – someone leaks Brody’s confession to the media.
Now that he’s the most wanted man in the country, Brody leaves the U.S. as Carrie stays behind in order to prove his innocence.
After the Langley bombing, Carrie is being held responsible for the CIA’s failings and we’re led to believe that even Saul, who is now the Acting Director of the CIA, turned against her. However, it’s revealed that the two are working together to make the CIA disavow Carrie so that she could trick a senior Iranian Intelligence into helping the Americans. The Iranian, who financed the Langley bombing, gives them information about the real culprit. Eventually, the CIA is able to capture him and prove Brody’s innocence.
Meanwhile, Brody is being held prisoner in Venezuela, where he is shot and becomes a heroin addict. After days of torture, Saul rescues him and cleans him up in order to recruit him for a new mission. Saul wants to use Brody’s notoriety as the “Langley bomber” to assassinate the head of the Revolutionary Guard named Danesh Akbari, who is in Iran.
Before he leaves for his mission, Carrie tells Brody she’s pregnant with his baby. Brody goes to Iran and seeks asylum. He is taken to meet Akbari, but fails to kill him at first. Meanwhile, the CIA puts out an order to kill Brody; Carrie helps him escape. Brody continues his mission anyway and murders Akbari by himself. Shortly after, Carrie takes him to a safe house. However, the new CIA Director gives up his location to the Revolutionary Guard. The season ends with Brody being publicly executed in front of Carrie, leaving her devastated.
Months later, after giving birth, Carrie is appointed as CIA station chief in Afghanistan, where she coordinates drone strikes. Sandy Bachman, a Pakistani station chief, tells her that a highly wanted terrorist, Haqqani, is hiding out in a farmhouse not far away. Carrie orders a strike on the farmhouse. As it turns out though, a wedding party was being held there and 40 civilians end up dead. Carrie heads to Islamabad where someone leaks Sandy’s name to the press, putting him in danger. The Pakistani station chief is then lynched by an angry mob right in front of Carrie and Peter Quinn.
Carrie returns to the U.S., where she spends some time with her daughter. She struggles with her new maternal responsibilities; eventually, she decides to leave the baby with her sister to go back to Islamabad. Quinn and Carrie believe that there’s a bigger conspiracy behind the recent events that transpired and decide to get to the bottom of it.
In Islamabad, Carrie works with a trusted ally, Fara, to contact Haqqani’s nephew, Aayan Ibrahim. While following Aayan, Fara discovers that Haqqani is still alive, which proves Carrie and Quinn’s theory. Carrie seduces Aayan to gain his trust, so he would lead them to Haqqani. Meanwhile, Saul is kidnapped by Haqqani’s men.
Carrie sets up a meeting between Aayan and Haqqani during which she’s planning to kill Haqqani. However, she discovers that the terrorist is aware that he’s being set up. Also, he brings Saul along to the meeting, for protection. Haqqani shoots his nephew in the head and flees.
The ISI orders the CIA to release several dangerous prisoners in exchange for Saul’s life. The CIA agrees to this arrangement, despite the fact that Saul would prefer to give up his life in order to defend his country. After the exchange, when they’re on their way back to the American Embassy, Carrie and Saul are struck by two RPGs. Simultaneously, Haqqani and his soldiers attack the embassy. It’s revealed that Haqqani is after a brief with the names of all the CIA informants in Pakistan. During the operation, Haqqani executes many embassy officials, including Fara. Quinn is able to wound Haqqan, but the terrorist still manages to escape with the classified information.
Later, Quinn decides to go rogue and plans to kill Haqqani himself. Carrie is able to stop him at the last minute, then tries to assassinate Haqqani herself. However, she changes her mind when she sees the CIA black operations director, Dar Adal, inside Haqqani’s car. Instead, Carrie returns to the U.S., where she tells Saul about Dar Adal.
Saul confronts Dar Adal, who confesses he made a deal with Haqqani; the CIA took Haqqani off their “kill list” in exchange for Haqqani agreeing to stop harboring terrorists in Afghanistan. Also, Dar Adal was able to obtain the video of Saul as Haqqani’s prisoner, which could potentially damage Saul’s political career and public image. He also asks Saul to once again lead the CIA, who reluctantly accepts. The season ends with a furious Carrie, as she finds out about her mentor’s shady arrangement.