Lincoln (Dominic Purcell) is still in Panama with Sofia (Danay Garcia) and LJ (Marshall Allman) when Michael calls him. They discuss the recent events in Sona: the prisoners rioted, burning the place down and allowing T-Bag (Robert Knepper), Sucre (Amaury Nolasco) and Bellick (Wade Williams) to escape. Michael also asks about how sure Lincoln is that Sara is dead. After the conversation, Michael is contacted by Mahone (William Fichtner) and Whistler, who are secretly working with Homeland Security to destroy the Company. Key to this plan is the Card, codenamed "Scylla", which contains information on all the Company's agents and operations, but can only be decoded from within an unknown facility. Whistler again hints that Sara is still alive when Wyatt arrives and attacks them, killing Whistler and retrieving the original copy of Scylla. To learn the truth, Michael travels to Chicago and contacts Sara's friend Bruce Bennett to find out for sure whether Sara is still alive, but gets caught by the police. Meanwhile, Lincoln, Sofia and LJ are attacked by a Company agent. Lincoln kills the assassin in a fight, and gets arrested by the Panamanian police. Mahone returns to the home of his family, only to discover that Wyatt has murdered his son. Since he is still wanted in the United States, Mahone is immediately arrested as well.
Michael and Lincoln are reunited in custody by Agent Donald Self (Michael Rapaport). Self is the Homeland Security agent who was working not only with Whistler, but with Aldo Burrows, in order to take down the Company. Unable to trust people within the government, Self arranges to have Michael and Lincoln be part of an unofficial, off-the-books operation to recover Scylla from the Company, with their freedom guaranteed when it's all over. The brothers refuse the offer. Bruce pays their bail, and when they're released, he reunites Michael with Sara, who has been hiding out from the Company in Chicago after being tortured by Gretchen. When Wyatt attacks the group at their supposedly-secret hideout, Michael, Lincoln and Sara decide to join Self's team, believing that they can only be safe once the Company is destroyed. Also drafted into the team is Mahone, Bellick and Sucre - who were captured while trying to visit Sucre's baby girl.
In a subplot, T-Bag is making his way from Panama to the United States, looking for Michael in order to get his revenge. He tries to get to San Diego, following direction written in Whistler's bird book (which, unbeknownst to him, contains information on where to decode Scylla), but his drivers steal T-Bag's money and abandon him in the desert with their overweight companion.