After Mike's shooting, Ryan and Parker try to get around Nick to take down the people that organized the attack. Meanwhile, Carroll turns to an unlikely ally for help in finding Claire's location in protective custody.
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The team attempts to rally behind Captain Cragen after he comes under investigation for the death of the escort beside whose body he awoke. Unfortunately, they are hampered by an aggressive district attorney and a replacement captain whose management style differs greatly from Cragen's.
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The team investigates the death of an underage escort who died during a raucous bachelor party with VIP guests. The trail uncovers publicity-shy attendees, a fight for supremacy between two escort services and an old friend of the squad.
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After a wealthy woman dies of a heart attack, Danny and Jackie must investigate when her daughter claims God told her that her stepfather actually murdered her mother. When the archbishop comes asking for Frank's support for the canonization of a local priest, Frank decides to check into a rumor about the priest back when he protested the Vietnam War.
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In the penultimate episode of the first season, the truth about Brody's plans are revealed, and the stage is set for the final episode, where Brody will be revealed either as a war hero/politician/devoted family man, or a terrorist. Carrie is close to figuring out the truth, but her plans are derailed when she must deal with her own medical condition and career path.
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The relationship between Carrie and Brody becomes more complicated when they head into the countryside for the weekend, while Mike and Jessica face the fallout of the truth about their relationship, and Saul catches Aileen on the run to Mexico.
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An undercover agent hands over new evidence to Carrie who is keeping an eye on the surveillance footage of Brody's home.