As the fourth season opens, Michael is in L.A., looking to even the score with Gretchen for Sara's death, while Gretchen, Whistler and Mahone go about Company business. And in Panama, Sona has burned to the ground, with T-Bag, Bellick and Sucre unaccounted for. Meanwhile, Lincoln, LJ and Sofia are settling in as a family. Wyatt: Cress Williams. Pam Mahone: Callie Thorne. Don Self: Michael Rapaport.
Michael and his crew have one day to find the other five cardholders or they'll go back to prison. But Mahone is obsessed with seeking vengeance, and Michael and Linc fear that he's losing focus. Meanwhile, Wyatt (Cress Williams) has Bruce Bennett in his custody, and is using a truth serum to find the crew's whereabouts; and T-Bag finds the gateway to his new identity and his future.
The crew tracks another card down to the Turkish consulate in Los Angeles, but the cardholder isn't the consul. Meanwhile, Wyatt arrives in L.A. with information about Sara he had extracted from Bennett; Michael and Linc happen upon T-Bag by chance; and Bruce Bennett is found dead.
Don Self tracks down another card to a safe in a heavily guarded Los Angeles federal office building while Mahone gets a few leads in his efforts to track down Wyatt, who chases Sara and tortures Gretchen. Meanwhile, Sucre and Bellick try to track down T-Bag, who makes another discovery about the bird book as he quickly raises suspicions at GATE.
After successfully transcribing the fourth card at an L.A. racetrack, Mahone is arrested---with the transcribing device on him---for being in a restricted area (and for punching a cop). Meanwhile, the Company hones in on Don Self; T-Bag's boss at GATE finds more "irregularities" in his sales reports; and Gretchen surfaces at her sister's tidy suburban home.
While Linc, Sara, Sucre and Roland track down the fifth card in Las Vegas, Michael and Bellick are unavoidably detained in L.A. by a gun-wielding T-Bag, who needs Michael to decipher the bird book. T-Bag, as it happens, is doing the bidding of Gretchen, who made him an offer he couldn't refuse. Meanwhile, Wyatt shows up at Don Self's home; and Sara learns something disturbing about Michael. Scuderi: Jude Ciccolella.
While Pad Man lays out the Company's next gambit to his underlings, Lincoln reaches into his past for a way to gain access to the final card, which is in Pad Man's possession, and Michael and Self have a meeting with their colleague-to-be: Gretchen. Meanwhile, Roland seethes at the treatment he has gotten from the gang since he lost the transcribing device in Las Vegas.
While Michael, Linc, Bellick and Sucre navigate the GATE basement looking for a way to break into Company headquarters, a police detective upstairs questions T-Bag about Andrew Blauner's disappearance. Meanwhile, Gretchen has a meeting with Pad Man; Wyatt has a proposal for Sara (which Self records) and Mahone waits for his turn with the Company hit man.
Gretchen gives Michael the rest of the bird book, but he suffers another seizure after deciphering it, so the others must carry out his two-pronged plan: one leading back to the basement, the other to an architect named David Allen Baker (Keith Szarabajka). Meanwhile, Pad Man goes forward with his plan to move Scylla, and Self is told by an influential senator that the deal Homeland Security made with the gang is "off the table."
While Gretchen focuses on getting the sixth card and Lisa Tabak finalizes plans to move Scylla, the gang penetrates the room where Scylla is still located. But that's only half the battle. Meanwhile, Michael reluctantly agrees to see a specialist; and T-Bag's boss at GATE makes him a tempting offer.
As the hunt for Scylla concludes, Sarah takes a hostage, T-Bag and Gretchen have their last stand at GATE, and Michael and Lincoln encounter Gen. Krantz. They're also betrayed by one of their own.
As Michael, Linc, Sara, Sucre and Mahone regroup, Gen. Krantz reasserts his control of the Company in no uncertain terms as he scrambles to regain Scylla. Later, T-Bag gets a new partner in crime, and Michael and Linc have a critical meeting with Sen. Conrad Dallow (David Clennon).
While the gang continues to match wits and blows with Self and Gretchen for control of Scylla (and with the Company in hot pursuit), Mahone enlists the aid of former FBI colleagues Lang and Wheeler (Barbara Eve Harris, Jason Davis). Meanwhile, Sara raises the dosage of the drug she's giving Michael to counter the effects of his brain tumor, and T-Bag continues to hold Gretchen's daughter and sister prisoner. But T-Bag tells Gretchen's sister: "I'm as much a prisoner as you."
Following Linc's deal with the devil, Michael has his brain operation. Linc also extracts information from T-Bag, with whom he was recently reunited. Meanwhile, Wheeler and Lang transport Mahone to prison; and as Self and Gretchen await their prospective customer, Gretchen gets a phone call from her sister that's both reassuring and troubling. During surgery, Michael (who's conscious) gets unlikely help in unraveling the mystery of Scylla. Westmoreland: Muse Watson.
While Linc and his new colleagues are in hot pursuit of Scylla in Miami, Michael is at a remote mountain cabin in California, where he learns something new about the Company. He's also guided through childhood memories by a Company psychiatrist (John Getz). Meanwhile, Sara is waiting for news of Michael in a luxury hotel, and she's not enjoying the luxury. Christina: Kathleen Quinlan.
Michael and Sara hitchhike to Miami, and Lincoln meets with Christina (Kathleen Quinlan), who tells him of her plan to take over the Company and warns him not to meddle in it. Meanwhile, a new foe challenges Pad Man, and T-Bag and Self find something they weren't expecting when they search for Scylla.
It's Linc vs. Michael over Scylla as Christina (Kathleen Quinlan) sets her plan in motion and a sniper targets Linc. Meanwhile, Sara receives some news; T-Bag makes his presence known at the Indian embassy; and Pad Man's paranoia intensifies.
Michael arranges to meet Christina. It isn't an easy reunion to begin with, then she says something surprising about Lincoln. Meanwhile, Pad Man arrives in Miami with a nonnegotiable demand for his new operatives; Linc races to abort Christina's plan; and T-Bag must prove his trustworthiness to the Company.
As Christina's plan is executed, Michael and Linc are stuck at the Miami hotel where the energy conference is being held. Later, Pad Man makes good on a threat, and Michael must choose between Lincoln or Sara.
In the series finale, old friends (Amaury Nolasco, Rockmond Dunbar) turn up as Michael makes one last effort to rescue Linc and Sara, get Scylla into responsible hands and take down the Company---all while on the lam. Sofia: Danay Garcia. Lang: Barbara Eve Harris.