Ricardo is discovered to suffer from Alzheimer's; Beecher flips out and sends Schillinger to the hospital; mob boss Schibetta develops stomach problems thanks to some ground glass; and Said has a heart attack.

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 an officer by mistake.

After a visit with his sons, Schillinger realizes he needs to get paroled. He convinces McManus to let him return to Em City with the condition that he leaves Beecher alone. Beecher comes out of the hole hell-bent on making sure Schillinger doesn't get paroled. McManus gets wind of Wittlesey and Ross' contraband operation and orders her to shut it down. Ross makes it very clear to her that this will not happen. The Muslims meet and discuss how the riot will begin. However, two rednecks beat them to it by fighting over a game of checkers. This causes all the inmates to get involved and they quickly overpower the COs who are trying to break it up. Said orders the Muslims to get out and seize control. Said pulls out the gun he acquired from a rookie CO and fires a shot into the air, causing Em City to quiet down. Said meets with Ross, Adebisi, O'Reily and Alvarez to discuss strategy and demands. Said agrees to let O'Reily, Ross and Adebisi control the main gate and Alvarez will control the hostages. Dobbins was seriously injured during the initial uprising and Hill convinces Vayhue to step up and help. Vayhue and Dobbins leave Em City only to be beaten up by SORT. The hostages require medical attention, so Alvarez and Said vote in favor of a doctor. However, Adedisi, Ross and O'Reily vote no. Governor Devlin orders the National Guard to surround the prison and take it back, but Glynn and McManus think they should see the demands first. McManus volunteers, to Devlin's disgust, to enter Em City to deliver food and check on the hostages. He tries to get COs Armstrong, Mineo and Wittlesey free in exchange for himself. He gets Armstrong and Mineo released, due to their injuries but Wittlesey has to stay. After reading the demands, Glynn realizes that the prisoners are being quite reasonable, however Devlin orders the National Guard and SORT to re-take Em City anyway. Meanwhile Ross' men and Adebisi's are constantly fighting, so Said tells O'Reily to switch Ross' men with Alvarez's at the front gate. A short tie later, Adebisi's men start to fiend due to the depletion of heroin, resulting in a major skirmish. Just as that situation is resolved and the Homeboys are tied up, the lights go out. Said realizes the situation and orders Ross to bring out the hostages as a front line of defense. Soon tear gas is thrown into Em City, then a tractor breaks through the barricade and gunfire rings out in Em City.

Season Two premiere. 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.

Morales looks to pit the Chinese against Redding. Alvarez offers Glynn his services as an informant as a way out of solitary. Dr. Nathan announces that Em City inmates will be selected to test a trial drug that could reduce their time behind bars.

O'Reily regrets getting Cyril involved with the trial drug when it starts taking effect. Meanwhile, Giles' request for an unusual execution creates controversy and the Chinese refugees are deported...but not before plotting revenge on Morales.

O'Reily is in for a surprise when a visitor reveals the truth about his past, while Cyril faces trouble for his difficult behavior. Meanwhile, Morales and Redding lay out plans that could lead to all-out war in Em City.

McManus calls a superficial truce between Redding and Morales. Basil finally sees his wife, but Hughes ends up spoiling their happiness. Meanwhile, Cyril's latest outburst proves to be the last straw.

McManus can't turn his back on White. Beecher tells the parents of the girl he killed that he's up for parole. Howell tries to blackmail O'Reily so she can get to Cyril, but he throws her for a loop--and then O'Reily is thrown himself by a secret.

In the Season Four finale, Hill discovers where his true allegiances lie in Oz. Redding's plot to use the Colonel against Morales has an unexpected outcome. Beecher's agony about his parole hearing leads to a shocking season climax.

Querns is appointed the new warden of Oz. Brass attempts to get famous for a day. Tim tries to change the mindset of Said's murderer. Cyril is finally executed. Keller brings Tobias back to Oz for good.