"Brother's Keeper" is the sixteenth episode of the first season of Prison Break and the sixteenth episode overall. It was written by Zack Estrin and directed by Greg Yaitanes. This episode is a flashback episode featuring the events which happened three years prior to the incarceration of the protagonist, Michael Scofield. It covers the actions of the characters Lincoln, Sucre, T-Bag and C-Note, which ultimately led to their incarceration at Fox River State Penitentiary. The reason behind Dr. Sara Tancredi's choice in accepting a job at Fox River and the basis of Michael's ingenious break-out plan are also revealed.
The opening scene shows Lincoln and Michael's strained relationship and Michael's bitterness against his brother. After Michael leaves, Lincoln meets a company agent at his old junky apartment and is told that, in order to pay off his debt of $90,000, he has to kill Steadman. However, Lincoln isn't told that it is Steadman, the Vice President's brother. Hours later, at the parking lot, just before Lincoln pulls the trigger, he realizes that he was framed. As he runs from the parking lot, Kellerman and Hale are watching the security camera footage. Later, Kellerman stands behind a technician as he digitally fakes a gunshot showing Lincoln pulling the trigger and framing him for the murder. After Lincoln's arrest, Michael conveys his disappointment about his brother's behavior. However, Lincoln insists that he never killed Steadman. Michael informs him that everyone thinks that Lincoln has motive to kill him because he was fired from a warehouse owned from Ecofield the company owned by Steadman.
Veronica Donovan reproaches Michael for misunderstanding his brother and that Lincoln may not be the man Michael thinks he is. She reveals that the $90,000 debt that Lincoln owed was given to Michael, because he thought Michael deserved it. Lincoln had lied to Michael about the money when he gave it to him, saying it was their mother's life insurance. After being found guilty and sentenced to death, Lincoln is scheduled to be transferred permanently to Fox River where he will be incarcerated until his death. Filled with guilt and familial obligation, Michael begins to formulate his intricate plan to break his brother out of Fox River such as remembering the blueprints and getting a tattoo which has hidden symbols of the blueprints and other significant details.
On the same night as Terrence Steadman's "murder", Sucre meets Maricruz Delgado and falls in love with her. Deciding that he was going to propose to her, he wants to find a way to get an engagement ring. He was arrested when he was caught committing his second robbery at a liquor store. For this reason, Sucre was sent to Fox River. The camera pans out to show that his cousin, Hector Avila, had phoned the police.
T-Bag arrives for dinner at his girlfriend Susan Hollander's home with two children. As he teaches the little girl her times tables, his girlfriend sees on America's Most Wanted that T-Bag is wanted for 40 counts of kidnapping, rape, and first degree murder. He is sent to Fox River after his girlfriend turned him in. During a later visit with Susan in prison, T-Bag reveals to her that he felt 'real love' for her in prison and that he had tried to change and repent for his actions; however, his turn to prison had caused "that old dirty bastard [to come] right back home."
C-Note was dishonorably discharged from the army by his commander after he filed a report of injustice against another soldier who was torturing a prisoner. The commander had him discharged for black market dealings. After coming home, C-Note could not find employment. He reluctantly accepts a job suggested to him by his brother-in-law, that involved illegal activities. He was arrested after driving a truck loaded with illegal goods. With his impending imprisonment, C-Note lies to his wife about serving overseas again. C-Note tells his brother-in-law that he should take good care of his wife and daughter. He emphasizes that he does not want them to know that he is going to be incarcerated in prison.
Dr. Sara Tancredi is first shown injecting herself with morphine from the hospital. After work, she walks on the street in a residential neighborhood with her boyfriend. Suddenly, a boy is hit by a car. When Sara approaches the boy, another witness asks for her help after noticing her hospital staff ID but Sara was unable to help him because she was impaired by the drugs. This incident haunted her. 18 months later, at a meeting for former drug users, Dr. Tancredi reveals to the other ex-addicts that the best thing for her rehabilitation is to go back to work, and that she had never been happier; she felt joy. After the meeting, Bellick goes up to Dr. Tancredi and awkwardly asks her out by saying that there was a job opening at Fox River State Penitentiary, where he works, and that they can talk about it over dinner. Sara politely declines his offer and thanks him for letting her know about the job, subtly conveying her interest.
As Lincoln runs from the parking garage, Kellerman and Hale are filming the whole thing. Later, Kellerman supervises a tech who doctors the tape to make it look like Lincoln is the shooter. Kellerman and the Vice President then discuss the purchase of a secluded mansion in Blackfoot, Montana for 2 million dollars. We learn that Kellerman is very affectionate towards Reynolds. She tells Kellerman to use the money left for her in her brother's will because she is cleaning up his mess. Vice President Reynolds then relays the fact this secluded mansion is bought for herself and "someone else". At the newly purchased mansion, she tells this "person" that Lincoln will be finished. This "person" puts on his false teeth, turns around and says, "My dear sister, you have no idea what I've been through". The person turns out to be Terrance Steadman, living alone.
The episode finishes off with a final shot of Michael hesitantly reaching for the two guns that he will use to rob the bank.
- Sucre sees Maricruz for the first time because Lincoln bumps into him on the street and spins him round, while running from the scene of the crime.
- The melody heard in the liquor store Sucre robbed is Francis Lai's theme melody for the film "A Man and a Woman" (1966).
- This is the first episode that is not in present. This flashback goes 3 years back, before Lincoln, Michael, Sucre, C-Note and T-Bag were in Fox River.
- John Abruzzi appears only on pictures, but not in person.
- L. J. Burrows doesn't appear.
- This episode marks the first appearance of Susan Hollander.
- This is the first episode to show two prisons: Fox River and an unnamed prison.