Three generations of Alvarezes--all prisoners at Oz--are united when the partiarch, Ricardo, is found face down in his cell, suffering from Alzheimer's disease. Meanwhile, Tobias Beecher, who as the neo-Nazi Schillinger's "girlfriend" has been forced to wear women's clothes, flips out after taking PCP and sends Schillinger to the hospital with an eye cut. Other inmates aren't exactly the picture of health, either. Mob boss Schibetta has stomach pains caused by ground glass intentionally mixed in with his food, and Muslim leader Kareem Said has a heart attack after refusing to take medication for high blood pressure.

A recovered Said ostracizes Huseni Mershah for turning his back on him when he was dying--and orders all the Muslims to cast him out. Impressed by Said's power, Groves decides to kill Glynn in his honor, but ends up stabbing and killing an officer by mistake. Condemned to death, Groves chooses the firing squad as his form of execution. Meanwhile, Schibetta is still being fed ground glass by O'Reilly and Adebisi, and ends up hemmorhaging. Beecher, transformed by prison life, finally gets revenge on his nemesis, Schillinger.

Beecher is released from the hole and Schillinger is left eyeless and weak. A riot breaks out after two white punks get into a fight over checkers. Frustration, sexuality, hate, revenge, racism all rear their ugly heads, causing the violence to escalate. Finally, after several prison officers are taken hostage, tear gas is thrown into the Emerald City and the SORT team arrives, guns blazing.

In the aftermath of the riot that killed six inmates and two officers, Oz is locked down, and Emerald City prisoners are sent either to solitary or "gen pop." A special committee is appointed to investigate the riot and Governor Devlin's handling of it. The committee's leader is law-school Dean Alvah Case, who roams Oz questioning inmates and officers alike. Inside a gen-pop prisoner named James Robson demands that Beecher perform oral sex on him, and gets a painful tip in return. Case determines that the death of inmate Scott Ross during the riot was no accident-but is the truth better left untold?

Alvarez knows who raped Glynn's daughter, but refuses to tell the warden. Wangler is making progress at school, but his cellmate, Adebisi, isn't a fan of higher education. When Augustus Hill's judge is convicted of accepting bribes, Said takes up Hill's case to get him a second trial. Diagnosed with cancer, O'Reily goes to a hospital to get a prison-paid lumpectomy, which is cheaper than a mastectomy. The Aryans are losing credibility in Oz, so Schillinger arranges to have a tough named Vogel killed with Beecher being the next on the hit list. Finally, the prison is filled with excitement as a woman, Shirley Bellinger, arrives on death row to be executed.

Cyril O'Reily, Ryan's brother comes to Oz and is immediately violated by Schillinger. Ryan tries to get him away from OZ, but Cyril instead lands in the hole. El Cid tells Alvarez the only way he can "stay in the game" is to "pluck out" the eyes of a prison guard, Rivera. Bellinger and Adebisi exchanging love letters without meeting. Nappa, the new Wiseguys leader, wants Adebisi to be punished for raping his godson Peter Schibetta. Robert Sippel, a Catholic priest who spent ten years in OZ for molesting a 14-year-old boy is released and but Poet returns.

Wittlesey is transferred to Gen Pop and replaced by Karl Metzger, a Nazi. Mack and another Aryan try to escape through Busmalis and Rebadow's tunnel but the tunnel collapses and kills the two Aryans. Hill gets the idea of escaping Oz by hiding in a coffin. Sippel re-enters Oz because he can't deal with life on the outside, but Schillinger crucifies him -- literally. Alvarez gouges out Rivera's eyes and is put in solitary for life. Needing a blood transfusion for Rivera, Dr. Nathan finds that only O'Reily has the same blood type; he agrees to donate in exchange for getting his brother Cyril near him. Keller and Schillinger reveal their sordid plan of deceit to Beecher while breakingv both his arms and legs. Fortune teller Kipkemei Jara gives Adebisi hope of a new life; but he is murdered by Wangler on orders from Antonio Nappa. The grief this causes Adebisi lands him in the psych ward. Said is pardoned by Governor Devlin, but refuses choosing to return to Em City instead.

With a new day breaking, Officer Howell makes a gruesome discovery. Dr. Nathan takes action against medical official Garvey. Ricardo and Hughes have a brief confrontation that results in a reprimand. Said's attorney brings good news and a special delivery. Richie Hanlon explains to Shirley Bellinger why he's on death row. New prisoner Stanislofsky joins the fold. Each group in Oz prepares their boxer for upcoming matches. Hill returns from testifying against Coyle, and the jury's still out as to whether or not that was the smartest move. Said solicits assistance from Nappa, Schillinger and Guerra. Nappa turns over control to Pancamo after discovering he has a debilitating illness.

After getting pummeled by Khan in a boxing match, Kenny discovers his wife's infidelity and arranges a contract. Miguel prepares to meet his victim face to face. McManus' lawsuit starts taking it's toll as he wrestles with settling or going to court. New inmate Kosygin is mysterious at best and Stanislofsky keeps a safe distance. Busmalis gets a surprise in the mail. Hughes presses Glynn for more information about past deeds. Beecher and Andrew form an alliance that angers Schillinger and Poet and Junior get a hot reception.

Sister Pete's anger is roused and forces her to confession. Wangler and Adebisi register a complaint to the Warden. Yet another inmate meets with demise. Bellinger enlists McManus' help. Glynn and Hughes have an important conversation. Adebisi begins sowing seeds of discontent and a fight erupts in the gym resulting in a lockdown.