Season 3

Complete listed story — includes the ending

1. The Truth and Nothing But...

The prison is renamed Oswald State Correctional Facility Level 4. Governor Devlin makes a deal with Weigart, a pharmaceutical corporation, to cut costs to the state prison medical board. This results in Alvarez, who is suicidal, having his medicine rejected and his not being fed in retaliation for blinding Rivera. Wangler, who dubs himself "Brickz", takes new inmate Malcolm Coyle under his wing. Nappa who suspects he is undercover, decides to have Wangler prove his loyalty to him. Adebisi is released from the psych ward and decides not to fight back. Clayton Hughes, who is a close friend of Glynn, whose father was killed in the line of action, is hired. Another new CO, Claire Howell, sets her sights on McManus. O'Reily wants to get revenge on Schillinger by causing trouble between Schillinger and the bikers. Richie Hanlon is sent to death row, and Bellinger finds him intriguing. Said meets Scott Ross' sister to try to persuade her to join the lawsuit; during this meeting, he starts to show feelings for her. McManus learns the truth about Metzger and tries to get Beecher to testify about what happened to him. Beecher declines. Keller starts to feel guilty for his part and wants to prove his love to Beecher, so he confesses the truth to McManus. Beecher gets revenge on Metzger.

2. Napoleon's Boney Parts

With Metzger dead, McManus brings in a childhood friend, Sean Murphy, to become supervisor. With Murphy's help, McManus organizes a boxing tournament. Coyle, who is working in the barbershop, confesses a strange tale to Hill, who does not take the news very well. A lawsuit is in effect against the state. Said, who does not want his judgment about his faith clouded, decides to fast. McManus and Howell's relationship takes a turn for the worse. Hughes feels he does not have what it takes to be a C.O. Schillinger's son is arrested for possession of drugs. Keller is sent back to Em City, but Schillinger exacts his revenge on him. Adebisi ostensibly wants to work in the AIDS ward in hopes of learning about the disease, but his true motives become clear when he gets revenge on Nappa. Alvarez continues to show signs of agitation. Dr. Fredrick Garvey, who heads the organization administering health care at Oz, gives Dr. Nathan two weeks' notice for disagreeing with him. Mukada tries to comfort Alvarez by giving him food. When Alvarez refuses the food, the C.O.s once again take their frustrations out on him. Sister Pete decides to start a victim/offender program; Mukada wants the first session to be between Alvarez and Rivera. Glynn disagrees, and Alvarez attempts to end his pain the only way he knows how.

3. Legs

Following Alvarez's suicide attempt, Dr. Nathan decides to expose Garvey. Devlin instead exposes Garvey's past on the condition that Weigart revise its policies. Hill is in protective custody for exposing Coyle's murdering of a family. Said and other leaders want to protect Hill, but Nappa takes matters in his own hands. Said's efforts to practice his religion take another turn when he and the other Muslim prisoners go on a hunger strike. McManus and Glynn have no choice but to give in by allowing Said to have food in his cell. Howell tries to apologize to McManus for her actions. However, McManus still wants to break things off with her. After assaulting a prisoner, Howell is fired. The boxing tournament gets underway with Pancamo and Cyril winning their first matches. O'Reily fixes Cryil's fight to ensure that he will not be damaged more. Rebadow has diabetes. After he faints, he decides to meet his son and grandson, whom he has never met and who were unaware of his existence at Oz. Nappa discovers he is HIV positive and is transferred out of Em City. Keller continues to attempt to patch things up with Beecher. The arrival of Schillinger's son in Em City gives Beecher new hope that he will be able to get revenge on Schillinger.

4. Unnatural Disasters

Beecher befriends Schillinger's son as a means to get back at Schillinger. Howell sues McManus for sexual harassment and is reinstated. Said cannot fight his feelings for Patricia Ross. Keller manipulates Sister Pete after discovering why she became a nun. Rivera agrees to meet with Alvarez. Alvarez is released from Solitary. Once again, O'Reily uses his tricks to have a fight fixed. Hughes tries to earn respect his own way, which costs him his position in Em City. Hughes is transferred to the library. Hanlon's murder conviction is overturned. Nikolai Stanislofsky gets revenge but slits the wrong throat. Nappa decides to confess everything he has done in the course of his life. Adebisi recruits the Latinos to try to run with the Sicilians' drug trade. Wangler gets disturbing news that his son may be getting hurt and gets his comrades to take care of the matter.

5. U.S. Male

Hamid Khan defeats Wangler in the final first-round boxing match. In an act of revenge for the Homeboys, Poet delivers a poem attacking Said. Said's fellow Muslims also condemn him for continuing to meet with Patricia Ross. Said has a heated confrontation with them when he learns that Ross has received threatening messages demanding that she cut off contact with him. New inmate Yuri Kosygin, a Russian gangster, sparks animosity between the Sicilians and Russians when he declines Nappa's offer of friendship. Wangler learns that his contract has been carried out, and his wife and her lover are dead. While Wangler attends their funeral, Adebisi severely wounds Pierce and Poet, in a bid to regain control of the Homeboys. Adebisi returns to his old self. McManus prepares for his sexual harassment trial and is enraged when Dr. Nathan does not immediately agree to serve as a character witness. Officer Hughes begins investigating his father's murder and becomes aggressive while questioning Rebadow. Father Mukada witnesses the incident and offers Hughes emotional support, but Hughes declines. Beecher comforts and bonds with Andrew Schillinger, as he gives up drugs and goes through withdrawal. Beecher uses his influence over Andrew to taunt and threaten Vern Schillinger. Vern tries to improve his relationship with his son, but Andrew rejects him and white supremacy. After assaulting Vern, Andrew is put in solitary confinement, where Vern tests him by passing drugs to him through Officer Lopresti. Andrew cannot resist the drugs and suffers a fatal overdose.

6. Cruel and Unusual Punishments

William Cudney, who has been stealing chloral hydrate for Ryan O'Reily, realizes that O'Reily has been using it to drug some of the boxing contestants, fixing the matches. In order to save his own soul, Cudney plans to turn O'Reily in, but O'Reily hires Kosygin to "save him". With his brother's help, Cyril O'Reily defeats Pancamo in the next match. Stanislofsky attempts to bring Kosygin down, telling Pancamo that Kosygin has been fixing the boxing matches. Kosygin attacks Stanislofsky, almost killing him, but is stopped and taken to the hole. Nappa decides to write a memoir with the help of his new cellmate, Nat Ginzburg. Pancamo hears of this and decides that Nappa must be stopped, since his memoir might include confessions implicating the other Italians. At McManus' suggestion, Wangler enrolls in a parenting program and has a visit with his infant son, but he storms out when the baby seems uncomfortable around him. Adebisi, who is keeping Wangler tied up at night, plots to bring McManus down. Father Mukada takes up the investigation of Hughes' father's death, interviewing Giles, who tells him Glynn was the killer. Keller tries to repair his relationship with Beecher, but Beecher continues to rebuff him. Beecher goes to Said for spiritual counsel. Khan disagrees with Said's decision to include Beecher in their group; he rejects Said and takes over leadership of the Muslims.

7. Secret Identities

Alvarez meets with Rivera and his wife, but when they ask him why he mutilated Rivera, he does not fully explain his reasons. Sister Pete determines that Keller has been manipulating her, trying to earn her favor so that she might convince Beecher to forgive him. Realizing that she is sexually attracted to Keller, she decides to leave the convent. Carlo Ricardo, whose family has been visiting him since he came to Oz and started to whittle down, is put in solitary confinement for refusing to cooperate in an investigation of the drug trade at Oz; this causes him to miss his final visit with his sister, who is moving away. After Father Mukada confronts Glynn about Hughes' father's murder, Glynn finally tells Hughes what happened, confessing that his own foolish behavior with the inmates led to the fatal beating. Nappa completes his memoir, but Ginzburg secretly conspires with Pancamo, killing Nappa and destroying the memoir. McManus tells Whittlesey that he still has feelings for her; she kisses him in front of Claire Howell. McManus' legal problems worsen when Wangler makes a claim that McManus groped him, and Adebisi gets the media involved in the story. Bellinger's final appeal is denied, and after seeking McManus' advice about execution methods, she decides on a hanging. Soon afterward, though, an exam reveals she is pregnant. The final semi-finals boxing match sees Khan defeat Cramer by split decision. Beecher continues to explore Islam with Said, who recommends that he forgive Keller and Schillinger. Beecher and Keller reconcile, but Schillinger refuses to forgive Beecher and attacks him instead; Said and Keller intervene, setting off a melee between the Muslims and Aryans in which Beecher and Schillinger are stabbed.

8. Out o' Time

After refusing to tell Glynn who raped his daughter following the end of the meeting with Rivera, Alvarez is cast out and attacked by the other Latinos, but he defends himself, killing Ricardo in the process. He then tells Glynn that Ricardo was responsible for Ardith Glynn's rape. After hearing Bellinger's stories about her daughter being possessed by Satan, Sister Pete decides that Bellinger is mentally ill and convinces Governor Devlin to commute her sentence. This infuriates Bellinger, who had stated a desire to be executed. Ryan O'Reily is caught and forced to stop fixing the boxing matches with chloral hydrate, but he still manages to give Cyril an advantage in the final match, manipulating Cyril with thoughts of their abusive father. Cyril is so enraged that his knockout punch leaves opponent Khan brain dead. Cyril, who feels guilty about what happened, attacks O'Reily but breaks down. Khan's widow wants her husband removed from life support, but they refuse. She then threatens to sue the prison for negligence. On New Year's Eve, Racial tensions escalate amongst inmates and staff; Schillinger attempts to rally the white inmates despite their differences, while Adebisi does the same with the black inmates. Hughes begins to adopt Adebisi's views on race, and when he expresses these views to Glynn, Glynn fires him. Hill tries to stay out of the racial conflict, but when he is put in solitary confinement for defying Murphy, the inmates become more defiant. As the new millennium arrives, Glynn puts the prison on lockdown, and Adebisi finds a gun in his bed.