The story starts off with Sara being arrested for the murder of Christina (Scofield) Hampton, during her and Michael’s wedding reception. It is implied that surveillance video was altered by agents loyal to the General (Jonathan Krantz) (Leon Russom) by removing Christina’s gun to make it look as if Sara shot Christina in cold blood rather than self-defence. She is held in the Miami-Dade State Penitentiary, where overcrowding necessitates that the female prison and jail inmates are housed in the same building. Gretchen Morgan watches from a distance, having been imprisoned after the events in “The Sunshine State”. Sara is attacked as revenge by the Miami-Dade COs for having left the infirmary door unlocked, allowing the “Fox River Eight” to escape and eventual dismissal or suspension of several staff members of Fox River.
Across the yard is the neighboring men’s jail and prison, where Krantz and Theodore “T-Bag” Bagwell (Robert Knepper) are being held. T-Bag continues to help the general, even though the General claims poverty when asked to pay for contraband T-Bag gets him. The General contacts Gretchen and offers her $100,000 to kill Sara. When Gretchen does not get the job done immediately, it is offered as a bounty for whoever kills Sara. Sara is quickly poisoned with strychnine, but is given medical treatment in the infirmary that saves her life and pregnancy. The correctional physician informs her that she will have thirty minutes with her baby when she gives birth before the baby is taken away from her. His advice is to consider herself to be a surrogate mother to her own fetus so as to avoid crippling depression due to the inevitable separation.
Michael learns of the attacks from Sara’s lawyer, and asks the warden to protect her, which she declines to do. She also denies Sara visits from anyone except her lawyer. After learning about the bounty on her head, Michael decides the only way to keep her alive is to break her out. He once again enlists Lincoln Burrows (Dominic Purcell) and Fernando Sucre’s (Amaury Nolasco) help. Lincoln and Sucre scope out the prison, taking measurements and photographs to create a map of the prison. Gretchen sees Lincoln and Sucre, and demands Sara include her in any escape plan that may be developing.
After analyzing the photographs and plans of the prison, Michael finds a fault in the security system: a blind spot the cameras cannot see. Alexander Mahone (William Fichtner) then arrives and offers his aid, although his true intentions are unclear. He has just been offered reinstatement with the FBI if he finds and reports any evidence incriminating Michael.
Michael develops an escape plan which he relays to Sara using a hidden message in a letter. While he is out however, FBI Agent Todd Wheatley (Chris Bruno) breaks into Michael’s apartment, and sees the plans laid out on table. When Michael arrives, he points out that while the plans may look incriminating, he was merely looking for weaknesses to report to the prison warden (Amy Aquino) in the hopes that she may grant him visitation rights.