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.

Lincoln and his men (Self, T-Bag, Mahone) are trying to find Scylla. They try to find a clue for the key from the fake buyer who killed Gretchen. They find a Church and an Estate that matches with key. When Lincoln and Mahone investigate the Estate, Lincoln finds a picture of him with his mother. Mahone finds out that, picture was edited and some clue about meeting place. Lincoln takes the meeting and finds his mother. Christina wants 2 days from Lincoln for eliminating Krantz. By the way Company's men finds Michael and Sara, they run away with truck and escape again. At last Lincoln goes to meeting place again and beginning of the end starts.

Michael and Lincoln square off over Scylla as Christina sets her plan in motion. Meanwhile, T-Bag causes a scene at the Indian embassy.

Michael has an uneasy reunion with Christina, who drops a bombshell regarding Lincoln. Elsewhere, Lincoln races to stop Christina's deadly plan.

Pandemonium erupts at the Panda Bay Hotel after an assassination at the global energy conference.

As familiar faces return to help Michael in his quest to bring down The Company, Lincoln makes a discovery about his relationship with Michael.

After the general catches the brothers and raises the stakes by abducting more of their relatives, Michael escapes with Scylla.