Michael gains a necessary piece of information to effect his escape, but can he keep the Warden from kicking him out?

With the pipe to the infirmary replaced and Lincoln's life hanging in the balance, Michael must rethink his plan to escape and save his brother's life. A fellow inmate may hold the key to preventing Lincoln's execution.

Flashbacks provide exposition on how the inmates arrived at Fox River Penitentiary from The Company's framing of Lincoln to the creation of Michael's plan to save his brother's life.

Picking up from where we left off, Sucre, Michael, Linc, and Aldo are together, with Mahone on their trail. Sara is face-down in the bathtub as Kellerman prepares to dispose of her body. C-Note is in Harvey, North Dakota with Kacee and Dede, who needs her medication. In Tribune, Kansas, Detective Slattery questions Bellick.

The Border Patrol arrests Michael and Lincoln, saving them from Mahone that claims that wants his life back. Sucre crosses the border and jumps in a parachute in the Sonora Desert in Mexico. T-Bag goes to a war veteran bar in Pratt, Kansas, and steals a prosthetic job from a veteran sergeant. Michael and Lincoln are apprehended in the Border Patrol Holding Facility, in Las Cruces, New Mexico, waiting for transportation to Fox River, but Bill Kim orders Mahone to kill them. T-Bag meets Denise, who works in the post office, and seduces her to get Susan Hollander's address. Bellick is sent to the District Court in Greeley County, Kansas, and has his bail denied. He makes a deal to be sent to Fox River expecting to have a good life. However the new warden decides to use him as an example of the new administration. Meanwhile Mahone tries to transport the prisoners, but the standard procedure does not allow it. Kellerman makes an arrangement to intercept the convoy in a blocked tunnel to kill the prisoners. However, Michael and Lincoln and helped by a surprising allied. T-Bag finds Susan.

Lincoln calls Sara from Miami asking for news about Michael and tells that he is trying to retrieve the Scylla for The Company with Gretchen, T-Bag and Self. They find a lead in the Grafton Club, and Lincoln goes to the place where he abducts Tia Hayden trying to find the representative of the owner of Scylla. Meanwhile Michael awakes locked in a house in the woods under the surveillance of bodyguards of The Company. The psychiatrist, Dr. Roger Knowlton, tells him that his mother is alive and is working for 'The Company' in the Madagascar Rainforest. He wants to prepare Michael to join 'The Company' and use his skills on a global scale working with his mother. Tia lures Lincoln and manages to escape, but he keeps her wallet and finds her address. Sara tells General Krantz that she wants to stay with Michael, but he says no to her. T-Bag and Self go to Tia's house and Self plots against the Lincoln's leadership. They bring pictures and a HD they found in the house. Self argues with Lincoln and Mahone arrives to balance the situation. Michael sees pictures of his childhood and recalls his family reunion while Dr. Knowlton evaluates him for General Krantz and is pressed to use a quick and nasty process to force Michael to join The Company. Lincoln and Mahone go to the marina to investigate the representative of the owner of Scylla. Sara receives a mysterious cellphone message for a meeting and is abducted near a public phone by Lisa's men, and Lisa tells her that Michael is 60 miles northeastern downtown. Gretchen finds Scott, the representative of the owner of Scylla, while researching a database, but she lures the rest of the group and meets with Scott who promises ten million dollars for her. T-Bag overhears the conversation between Sara and Lincoln and calls General Krantz. He in turn orders Dr. Knowlton to drug Michael for transportation. However Michael reverts the situation and escapes running through the woods. Sara manages to rescue Michael. When the group meets Scott, there is a shootout and Gretchen is hit and left behind. In the end, the surprising owner of Scylla finally appears.