Orientación is the 45th episode in the series and the first in season 3.
As Michael and Mahone enter Sona's courtyard and witness a brutal fight between two prisoners which results in a prisoner's death, Lincoln tries to convince a clerk at the American Consulate to drop the charges against his brother and release him. The clerk explains to Lincoln, and the audience, about Sona: after violent riots a year previous, the prison guards pulled out of Sona and left the prisoners to their own devices. Since then, the prisoners have organised their own internal forms of leadership, economy and workforce and run the prison themselves. However, evidence uncovered by the Panamanian police is backing up Lincoln's claim that the killing of Bill Kim was self-defence, and the clerk is able to arrange a transfer for Michael to a safer facility until his trial.
The next morning, Lincoln stands in the office of the American Consul. The Consul is on the phone trying to get Michael out of Sona. The Consul tells Lincoln that Michael’s case looks like Michael will walk away an innocent man and he'll be transferred to another facility in forty-eight hours.
Within Sona, Michael is confronted by Mahone, who wants the pair to ally in order to survive within the prison, but Michael refuses because he can't get past the fact that Mahone shot and killed his father. Later, Michael and Mahone are among the new prisoners who are brought before Lechero, a prisoner who effectively governs the entirety of Sona and its residents. Lechero tells the new prisoners about their main rule: if one man has an issue with another, they are to fight to the death in an organised event. During the meeting, Luchero makes known that he is aware of Michael's history and is wary of the new prisoner. Soon after this, T-Bag enters the prison and immediately tries to integrate himself into Lechero's inner circle.
Bellick discovers that he is at the very bottom of the social strata within Sona, forced to clean the bathroom and perform other such tasks with another Costa Rican man which is in the same position as he is. After Sapo is killed in a prison escape attempt, he is contacted by another prisoner living in the sewers, and agrees to pass on a message in exchange for food.
A prisoner accuses Michael of stealing his stash of drugs - a set-up by Lechero - and challenges him to a fight, which Michael is forced to accept or else face Lechero's lackeys. In the frenzy before the fight, Bellick slips written messages into both Michael and his opponent's pockets. Mahone advises Michael to fight dirty, and Michael does once the fight commences, but even when his opponent is practically beaten he refuses to kill the man. The prisoner is slipped a shank and tries to stab Michael in the back but Mahone intervenes by attacking the prisoner, killing him. Since weapons were against the rules of combat in the event, Luchero is forced to let Michael and Mahone off. When the dead body is dumped outside the prison, a woman searches his pockets and finds the written message.
Meanwhile, Lincoln searches Panama City for Sara and is momentarily worried when the Chief of Police brings him to the morgue to identify a body, but it is revealed that it is not Sara's. Later, he is contacted by LJ, and goes to meet his son at a restaurant in Panama City. He is instead met by a representative of the Company. At the end of the episode Lincoln visits Michael at the prison and tells him what the Company had said: they had kidnapped both LJ and Sara, and unless Michael can break out of Sona with another prisoner in tow - Whistler, the man in the sewers - their loved ones will be killed.
- This is the only premiere and the only episode from this season not feature Fernando Sucre.
- "Orientación" is Spanish for "Orientation."
- This marks the first time that Mahone has killed someone in a premiere. He previously killed Charles Patoshik, David "Tweener" Apolskis and Agent Blondie, who apperared in the season 2 premiere, Manhunt; and he later kills Wyatt Mathewson, who appeared in the season 4 premiere "Scylla".