Season 5

Complete listed story — includes the ending

1. Ogygia

T-Bag is released from prison just as he receives a photo of Michael in a new prison. T-Bag shows it to Lincoln, who finds the hidden word "Ogygia", which is a prison in Sana'a, Yemen. Lincoln informs Sara, who has been raising her and Michael's son, Mike, along with her new husband Jacob, about Ogygia. She refuses to believe the news. However, Lincoln decides to travel to Yemen, asking help from C-Note, who has converted to Islam. Sucre offers to accompany Lincoln, who takes C-Note instead. The mysterious mercenaries who have been following and harassing Lincoln and Sara send Lincoln and C-Note's photographs to their contacts in Sana'a, where the duo overpowers the attackers and meets a contact, who exchanges a visit to Ogygia for Lincoln's United States passport. Lincoln learns that Michael's fake identity is Kaniel Outis, a dangerous terrorist affiliated with ISIL. Michael ignores Lincoln, claiming not to know him. Meanwhile, T-Bag is contacted by a physician offering him a prosthetic hand. T-Bag learns that an anonymous person known only as Outis funded the operation and insisted on him being the patient.

2. Kaniel Outis

Lincoln receives a coded message from Michael asking them to find the "Sheik of Light." Sheba, the contact, agrees to help decode the message in exchange for money. Sara receives the video recording of Michael and meets up with Kellerman at the State Department. He deduces that Michael was the mastermind behind changing his identity. Later, he sends Sara footage of Michael killing a CIA deputy director. Michael acquires pills to give to his cellmate, Ja, who is suffering from withdrawals in exchange for a cell phone and credit card, using them to send a message to Sara. Lincoln's team discovers that Mohammad El-Tunis, the Sheik, is a local electrical engineer trapped in an ISIL-controlled suburb with his daughter. They rescue the duo; and Mohammad is revealed to be the father of Sid, Michael's cellmate incarcerated for homosexuality. Mohammad gives Michael's team a signal to reveal that the escape plan is on. Sara receives Michael's message to get everyone to safety because "a storm is coming". The solitary inmates, including local ISIL leader Abu Ramal, are released into the general sector. Ramal and Michael are revealed to be friends.

3. The Liar

Lincoln prepares for the escape by ordering forged passports. However, he and Sheba are caught by ISIL and Cyclops, who attempts to rape her until Lincoln frees himself and saves her. T-Bag runs into Sara and tries to warn her about A&W and Van Gogh, two of Poseidon's henchmen, who may be following her trail. A&W and Van Gogh hack into her phone, later discovered by Sara, who deduces Kellerman's involvement. She asks T-Bag to investigate Kellerman. Cross, an inmate who refused to leave his brother Muza, and participate in Michael's escape, warns Whip that Michael cannot be trusted. Michael obtains a gold watch from one of the guards, planting it on Ramal, so that he will be detained during the escape. Michael and Whip are revealed to have been working undercover for the CIA as Whip worries the line between Michael and Outis will be blurred. During the escape however, Ramal's party, Cross and Muza race to Michael's cell and are caught by the guards, leading to Muza's death and the recapture of Michael's team. Ramal vows to kill Michael in solitary while Michael uses the last remaining battery life on his cell phone to record a goodbye to Sara.

4. The Prisoner's Dilemma

ISIL continues advancing in Sana'a. Cross rallies the other prisoners to capture Ramal and use him as a bargaining chip. Michael convinces a reluctant Ramal to help as he is the one inside the solitary cell with escape tools. Ramal, Michael, Ja and Whip are able to escape just as Cross and his followers break into solitary. Sid stabs Cross in the chest, joining Michael's party. They are all captured by ISIL. Ramal plans to behead Michael; but Lincoln intervenes and kills the jihadists while Whip kills Ramal. Michael and Lincoln share an emotional reunion as a news report on Ramal's death plays. Sid informs them that ISIL is now declaring war on them for Ramal's death. Meanwhile, T-Bag confronts Kellerman, who denies being Poseidon, a mysterious rogue CIA agent criticising U.S. foreign policy. They are attacked by Poseidon’s operatives. T-Bag manages to escape; but Kellerman is killed by Van Gogh, who starts doubting Poseidon's cause. T-Bag pursues A&W and Van Gogh and takes photos of them meeting with Jacob.

5. Contingency

Lincoln forces Michael to reveal the truth: Michael was contacted by Poseidon before his wedding with Sara; Poseidon revealed that Kellerman did not have any authority to exonerate Michael's team, offering legitimate exonerations in exchange for Michael faking his death, keeping the truth hidden from everyone and working for Poseidon. Michael's initial refusal led to Sara's arrest, after which Michael accepted Poseidon's deal. While Lincoln offers going to the airport and rendezvousing with C-Note's party, Michael decides to use the train station to leave Yemen. Cyclops works out Michael's plan and takes ISIL, intercepting Michael's party, who escape to a facility where Ja ambushes ISIL. They escape the building, but Sid is shot by Cyclops. Sid attacks Cyclops, but Cyclops stabs Sid, who handcuffs them together before he dies, leaving Cyclops handcuffed to his corpse, allowing the rest of the team to proceed to the airport. Meanwhile, C-Note's party arrives at the airport before ISIL attacks. C-Note and Sheba save a pilot, who agrees to fly them out of the country. They board a plane; but the pilot decides to fly before Michael's party arrives, which Lincoln approves of on the phone. C-Note's party takes off while Michael's is hunted by ISIL. In the meantime, T-Bag shows the photos to Sara, who confronts Jacob, who later attempts to prove his benevolence to her by having A&W and Van Gogh arrested.

6. Phaecia

Michael's party confronts Omar, who alerts ISIL; they overpower ISIL and force Omar's compliance, heading to Phaecia, a settlement in the desert capable of sending Michael's party abroad. A&W and Van Gogh are released on bail and convince an NSA insider to help track down Michael, whose party stops at a gas station, where Michael uses the internet to contact an unknown person in Portland, Maine, sending them a photo of the tattoos on his hands. Van Gogh alerts ISIL, who attack the gas station and kill Omar. Whip kills the ISIL operatives. Michael's party continues in the desert before learning about Cyclops chasing them. Michael takes one of the cars and lures Cyclops into a trap, where Michael blinds Cyclops' remaining eye. He is able to stab Michael with a poisoned blade. Ja helps the others find Phaecia, where they use fireworks to lead Michael to them, who falls unconscious after arriving. A&W and Van Gogh find Michael's contact, revealed to be an Elvis impersonator. Meanwhile, Agent Kishida replaces Kellerman, assigned to investigate his death.

7. Wine-Dark Sea

Ja decides to stay in Phaecia while the others leave on a boat to Crete, Greece. Lincoln calls Sara and tells her about Michael's condition. She informs Jacob and goes to Crete by plane. She reunites with Michael and heals him. He reveals that Jacob is Poseidon, having framed the former for the murder of the CIA official. Sara returns to the U.S. to secure Mike, whom she entrusts to her friend Heather; but they are captured by Jacob and his operatives. Michael reunites with Sucre on board the commercial ship upon which he is working. The captain learns about Michael and alerts the authorities. Navy SEALs are dispatched to kill Michael. Sucre formulates a plan to force the SEALs away, which causes an enraged Jacob to have a missile fired at the ship, which explodes just after Michael's party jumps overboard. Meanwhile, Kellerman's successor, Kishida, confronts A&W and Van Gogh for their clandestine operation, leading to the former's murder.

8. Progeny

Michael's party is rescued by a fishing boat that takes them to Marseille, France, where Michael contacts Sara, works out their situation, and decides to go to the US, using Lincoln's conflict with John Abruzzi 's son Luca over a failed smuggling operation to their advantage. Michael and Lincoln enlist C-Note and Sheba's help in disposing of Luca and his gang, then convincing C-Note and later Sheba to leave the conflict. They proceed with the plan of taking down 21 Void, a cell operated by Poseidon, and rescuing Sara and Mike, culminating in a lake house in Michigan, where Michael reunites with Mike but realises that it was a trap set by Jacob, and A&W confronts them, with an unknown person getting shot. Lincoln is found by Luca outside the house and is shot. Meanwhile, Whip, whose true identity is David Martin, is sent to Chicago by Michael, meeting T-Bag, who is revealed to be his father. The analyst Theroux is revealed to be a 21 Void agent, and Van Gogh expresses disdain for Jacob's methods and vows to leave 21 Void when the job with Michael is done.

9. Behind the Eyes

Van Gogh is revealed to be the one shot by A&W, having become skeptical of Michael's involvement in Gaines' murder. Van Gogh gives up Mike's location to Sara before dying. As Jacob works to brainwash Mike, Michael gathers his allies, including Blue Hawaii (the Elvis impersonator who Michael contacted in Yemen), to bring down Jacob. A wounded Lincoln escapes the hospital and ensures Luca's arrest by the FBI. Michael enacts a plan where he lures Jacob and A&W to a warehouse to recreate Gaines' murder and prove Jacob's involvement. During the attempt, Whip is shot by A&W and dies before T-Bag kills her and is arrested. Michael succeeds in proving Jacob's involvement and both are arrested. At the same time, Lincoln and Sara rescue Mike and capture Theroux. With the evidence planted by Michael and Theroux's testimony, Michael is exonerated and his identity as Michael Scofield is restored. He refuses an offer to join the CIA and returns to a normal life with Sara and Mike. Jacob is sent to Fox River State Penitentiary, where he ends up with T-Bag as his cellmate, as requested by Michael. The other inmates cheer T-Bag on as he attacks Jacob.