"Pilot" is the first episode of the first season of Prison Break, and the first episode overall. It first aired on August 29, 2005, back-to-back with the following episode, "Allen". It gained 10.5 million American viewers. The episode introduces the two main protagonists of the series, Michael Scofield (played by Wentworth Miller) and Lincoln Burrows (played by Dominic Purcell). The episode features the start of Michael's escape plan to save his brother from his death sentence.
Michael looks on as the tattoo artist finishes the final segment of his tattoo. Michael pays her, she remarks on the fact that it's rare for anyone to get a full body tattoo in such a short time. He returns to his apartment and starts ripping all his notes from the windows of his apartment, including "'Lincoln Burrows' Final Appeal Denied," "Governor's Daughter Wins Humanitarian Award," and "Life Sentence for Mob Boss Abruzzi." Michael then proceeds to disconnect and throw his hard disk off his balcony into the Chicago River.
Michael later holds up a bank, firing three gunshots. Michael points his gun at the employee and demand she open the vault, although she tells him that only the branch manager, who is at lunch, can open it and tries to convince him that he already has enough money (half a million dollars). As police arrive, Michael instantly puts his hands up. As ordered by the police, he throws his two guns to the floor.
After he is arrested, he goes to court, with his friend, Veronica Donovan, acting as his attorney. The judge remarks that it is odd for him to plead no contest. Veronica and the judge both tell him to reconsider, although Michael tells them he already has. He is then dismissed briefly for court recess. As he is being led back to his holding cell, Michael sees LJ, his nephew, and tells him to go home and that he didn't want him to see the trial. Veronica inquires him as too why he did it, but Michael simply tells her that he will handle it. He calmly accepts the judge's punishment of a five-year incarceration and seems pleased about it. Both Veronica and the judge are perplexed by his submission to the five year sentence. Honoring his request for a prison close to his hometown, Illinois, the judge places him at Fox River State Penitentiary, a maximum security prison. Veronica is alarmed by that but Michael dismisses her again.
Michael enters Fox River and is immediately disliked by Captain Brad Bellick and tells him that there are two commandments at Fox River: "you've got nothing coming to you" and "see commandment number one." When Michael responds smugly, Bellick reacts with hostility. It was then revealed to Bellick that Micheal suffered from Type 1 Diabetes. Michael observes the prison from his cell, earning the nickname "Fish". His cellmate, Fernando Sucre tells him to take a seat and that nobody will serve his time for him. Michael then witnesses one of the violent atrocities of prison life as a man is stabbed behind his back.
Outside in the yard, Michael takes notes of the people and surroundings around him. Michael proceeds to ask for the location of Lincoln Burrows. When Sucre asks him why he is so interested in Lincoln, Michael replies that he is his brother. At the chapel, Michael meets his brother and tells him that he is going to get him out of here. Lincoln promptly says that it is impossible, to which Michael replies, "Not if you designed the place, it isn't." As Michael sits in his cell, he remembers telling his brother to swear to him that he didn't commit the crime. He is convinced that Lincoln was framed for the murder of the Vice President's brother.
Micheal was then invited to help the warden, Henry Pope, to construct a Taj Mahal model made by toothpicks for Pope's wife. Soon later he meet Charles Westmoreland and his cat, Marilyn. Michael sits down next to him. Michael tells Westmoreland that he knew his wife. After testing Michael to ensure this new fish can be trusted, Westmoreland relaxes. Michael asks if Westmoreland is D.B. Cooper. Westmoreland smiles and replies, “Every new fish that comes in here, first thing they hear is that Charles Westmoreland is D.B. Cooper.” Westmoreland denies it. Abruzzi approaches, flanked by his goons. Westmoreland takes off.
Michael asks how to get into PI (Prison Industries), and Sucre tells him that it is controlled by Mafia boss, John Abruzzi. When Michael approaches Abruzzi, he is rejected. Michael calmly tells Abruzzi that he has something Abruzzi needs, and leaves an origami swan. Abruzzi realises that Scofield knows of Fibonacci and allows him to join PI. One of Abruzzi's friends asks "Why'd you let him in?" Abruzzi replies "Keep your friends close, and your enemies closer" after they broke into a fight earlier.
In Pope’s office, the warden threatens to throw Michael in the SHU for ninety days for fighting. But Michael thinks fast and offers to help fix the Taj instead of doing time in isolation. Pope agrees.
In the infirmary, Michael introduces himself to Dr. Sara Tancredi as she gives him his insulin shot. When he asks for her name, Sara tells him to call her "Dr. Tancredi" to which he swiftly replies, "Tancredi, like the governor?" She doesn't answer. Seeing her discomfort, Michael jokes that it's weird finding her working in the prison as a doctor when her father is "Frontier Justice Frank". Sara tells him that she wants to be part of the solution, not the problem. In her ignorance, Michael immediately recites her senior quote to charm her. On his second visit to the infirmary, Sara tells him that she graduated two years after him in a nearby university to his. Michael again tries to flirt with her. Sara suddenly notices his abnormally low glucose level and tells him that he is reacting to the insulin as if he is not diabetic. She then says that on his next visit, she would like to run a test. Michael looks worried. In the yard, Michael approaches C-Note, the prison "pharmacist" and pays him in advance for PUGNAc.
During PI, Lincoln asks Michael if he has seen the blueprints to the prison. Michael smiles and briefs Lincoln about the prison retrofitting job in 1999. Michael says, "I've got them on me." He reveals his mysterious body tattoo, which is a series of geometric patterns that disguise the blueprints to Fox River, on which Michael will base his escape plans throughout the series.
LJ and a friend ride their bikes through a dark alley. They follow a man to a car, where he opens the trunk and puts a large bag of marijuana into LJ’s backpack. But undercover officers are watching. Before the boys can flee, the police close in on them. LJ is being scolded by his mother, Lisa Rix. “Two pounds of pot? Were you trying to set a record?” LJ cracks a smile, but Lisa pounces on him. “It’s not funny LJ, you could be going to jail!” LJ’s step-dad, Adrian Rix, enters. Lisa says that LJ needs guidance, and LJ mutters that he certainly won’t get it from Daddy Warbucks. Lisa doesn’t understand why LJ is misbehaving, until she thinks about Lincoln. Maybe a face-to-face with his father will set LJ straight.
Sucre paces in the conjugal area, nervous that his girlfriend, Maricruz isn’t coming. A guard opens the door and Maricruz enters. She giddily accepts Sucre’s proposal. Sucre asks Maricruz how she got to the prison. When she answers, “Hector,” Sucre explodes. He doesn’t like Hector. He thinks Hector’s trying to steal her away. Maricruz tells Sucre that he has nothing to worry about.
Abruzzi's henchman Maggio talked to the butcher Gavin Smallhouse about Otto Fibonacci, a mob informant whose testimony put Abruzzi behind bars in Chicago. Soon after that, Abruzzi called Maggio. “You heard me. Someone found Fibonacci.” Abruzzi’s eyes light up and he wants to know who sent it. Maggio says he doesn’t know, but in the envelope was a “folded up bird.” This registers with Abruzzi and he hangs up the phone and walks away.
Special Agent Hale enters the office of Special Agent Kellerman. Hale tells Kellerman that everything is in place for Lincoln’s execution, except for Bishop McMorrow. Hale worries that the Bishop has a lot of influence with the Governor and may persuade him to grant a stay of execution. Kellerman realizes Hale’s point. “Maybe it’s time we arranged a visit with the good Bishop then.” Hale and Kellerman meet Bishop McMorrow at his home. Kellerman attempts to convince the Bishop to separate himself, no matter what, from Burrows’ case. The Bishop is firm; if an inmate on death row asks for help, the Bishop will intervene. Kellerman plays his last card, and accuses the Bishop of committing fraud. The Bishop stands strong and says he will not be bullied.
At night, the Bishop is fast asleep in his massive bed. A shadow moves across the wall. A floorboard creaks. “Who’s there?” he groans. He sits up, eyes wide. A gun with a silencer fires once.
Veronica Donovan meets her fiance Sebastian in Chicago. In Veronica's office, her assistant enters and tells her the news of the Bishop's murder. As it dawns on her that the one person who could have helped save Lincoln’s life has been murdered, Veronica mutters, "Michael was right." She removes a copy of Lincoln's trial deposition from a file cabinet.
- C-Note (Rockmond Dunbar) and Paul Kellerman (Paul Adelstein) are credited as guest stars in this episode, but would later be starring cast members later in the season.
- C-Note would be credited as main cast members from the 13th episode, while Kellerman would be credited as main cast member in the 3rd episode.
- Both C-Note and Kellerman would be featured in the last episode of season 4 as Special Guest Stars.
- This is the first episode that didn't show the whole main cast. This is also in Allen, Cute Poison, English, Fitz or Percy, Riots, Drills and the Devil, Part 1, Riots, Drills and the Devil, Part 2, End of the Tunnel, The Rat, Brother's Keeper, The Key, Tonight and Flight.