In the experimental unit of Oswald State Penitentiary, there are a diverse group of inmates who have their own groups. Although there is no one leader, after Kareem Said (who is a Muslim author that preaches non-violence, tolerance, and of all things abstinence) arrives to Oz, a Mafia inmate begins ticking off everyone, which ends up being his downfall.
The prisoners are visited by wives and other family. Meanwhile, Schibetta and the prison staff are on the hunt for Ortolani's killer.
After the death of Ortoloni and Johnny Post, Warden Glynn meets with gang leaders to tell them to stop the violence or the prison will be put on lock down. Meanwhile, Keane converts to the Muslim faith.
Governor Devlin reinstated the death penalty and Jefferson Keane will be the first person to be put to death in the state in 34 years. Before his execution, Keane donates his kidney to his sister. Later, serial killer Richard L'Italien is also put to death via lethal injection.
As the movement of drugs into Oz hits an all-time high, McManus and Glynn go undercover to find out who is getting the drugs into the prison but their plan backfires with deadly consequences. Despite the Emerald City being locked down, drugs continue to flow, which shifts the blame from prisoners to corrupted officers and staff.
The Alvarez family is united when patriarch Ricardo is found face down due to complications with his Alzheimer's disease. Tobias Beecher is forced by neo-Nazi Schillinger to wear women's clothing, but after taking PCP and going crazy, he cuts Schillinger in the eye, which sends him to the hospital. Health problems also occur in other parts of the prison -- Schibetta suffers stomach pains after glass is mixed in with his food and Kareem Said has a heart attack.
Kareem Said has recovered from his heart attack and ostracizes Huseni Mershah for leaving him for dead. Impressed by Said, Groves tries to kill Glynn in his honor, but kills an officer by mistake. Meanwhile, Schibetta is fed more glass in his food by O'Reily and Adebisi, which causes him to hemorrhage blood.
Beecher is released from the hole and Schillinger returns from the hospital, left eyeless after his fight with Beecher. During a game of checkers, a fight between two white prisoners sparks a riot, escalated by racial tensions. Prison guards are taken hostage, forcing Emerald City to be dowsed in tear gas and raided by the SORT team.
Following the riot, Oz remains on lockdown. Alvah Case heads up a committee to investigate the riot as well as the Governor's response and handling of the crisis situation.
Nearly a year after the riot, Emerald City is reopened. McManus assembles a group to keep order in Em City and begins a GED program in the prison for inmates. After learning that Adebisi killed his father, Schibetta takes over the kitchen. With Schillinger's parole hearing getting closer, Beecher begins to pester him as an attempt to ruin Schillinger's potential freedom. Meanwhile, Glynn's daughter is raped by Latinos and he takes his frustrations out on Alverez.
Alvarez learns who raped the warden's daughter, but refuses to tell him who did it. As Wangler begins to make progress towards his GED, Adebisi, his cellmate who isn't big on education, gets in the way. An opportunity arises for Hill to get a second trial when his judge is convicted of accepting bribes. O'Reily heads to a hospital to get a free lumpectomy after he's diagnosed with cancer. Schillinger puts out a hit on Vogel as the Aryans lose power in Oz, and Beecher is next on his list. Lastly, the prison is abuzz when a woman, Shirley Bellinger, arrives on death row.
Hill, who appealed his case, is denied a second trial. O'Reily is recovering from his lumpectomy and focuses his attention on Dr. Nathan. After killing an Aryan inmate, Richie admits to a murder he didn't commit while trying to cut a deal. Alvarez is offered a part in the drug business by Schibetta for killing Adebisi. Meanwhile, Beecher gets a new cellmate, Chris Keller, who also hates Aryans, but his appearance doesn't match his hate.
Adebisi poisons Schibetta, but not enough to kill him. Glynn has cleared his debt to Schibetta now that his brother turned himself in for murder. Poet is able to get parole and has his works published. Devlin discontinues the GED program by cutting funding. Beecher is told that his wife killed herself and Keller tries to offer support, but is efforts are turned away. O'Reily falls for Dr. Nathan and has his brother kill her husband.
Said is asked by Schillinger to help get him out of prison, but Said backs out. During the deposition, McManus lies to protect Wittlesey. Raoul Hernandez replaces Alvarez as the leader of the Latino gang. Following her husband's murder, Dr. Nathan confronts O'Reily.
Cyril O'Reily, Ryan's brother, arrives at Oz and soon after is raped by Schillinger. Ryan tries to help get him away from Oz, but ends up landing himself in the hole. Nappa, the new leader of the Wiseguys, wants to get revenge on Adebisi for raping his godson Peter Schibetta. A convicted Catholic priest is released from Oz, but Poet returns.
Wittlesey is replaced by Karl Metzger, a Nazi. Mack and another Aryan try to escape from Oz, but the tunnel collapses, killing them both. Hill comes up with a plan to escape by hiding in the coffin. Sippel comes back to Oz after he can't deal with life outside of the prison, but Schillinger literally crucifies him. Alvarez is put in solitary confinement for the rest of his life for gouging out Rivera's eyes. Lastly, Said is pardoned by Governor Devlin, but chooses to return to Em City instead.
Oz is renamed to Oswald State Correctional Facility instead of Penitentiary. Though hesitant, Glynn hires Clayton Hughes. In the prison, the newest correctional officer gets overly friendly with McManus. The new cheap health care angers Dr. Nathan and harms Alvarez. Meanwhile, Ryan plans revenge against Schillinger and Beecher is able to get revenge of his own.
When Metzger is killed, McManus hires Sean Murphy, an old friend to help supervise Emerald City. In another effort to curb violence, an inmate boxing program is established. Coyle confides in Hill about the gruesome manner that he killed a family. With the new health care system, Alvarez's medication has to be reduced, which causes him to start to go crazy.
First thing in the morning, Howell makes a shocking, gruesome discovery. Upset about the new health care, Dr. Nathan confronts medical official Garvey. Said's attorney comes with good news as well as a delivery. As the inmates prepare for boxing matches, Nappa learns he is suffering from a deadly disease.
Schillinger arrives to Oz and Vern tries to get him relocated to Unit B with him. McManus is sued for sexual harassment. When Said's sister visits Oz, he is forced to face the past. Hanlon's sentence is overturned.
Kenny is beaten by Khan in a boxing match and when he finds out that his wife has been unfaithful to him, Kenny arranges for her and her boyfriend to be killed. McManus has to decide whether to settle his lawsuit or go to court. Miguel readies himself to meet his victim. Meanwhile, a new, mysterious inmate, Kosygin, arrives at Oz and Beecher and Andrew form a bond that makes Schillinger angry.
While trying to deal with the guilt of killing Schillinger, Beecher goes to Said for spiritual guidance. Ryan O'Reily hires new inmate Kosygen to kill Cudney.
Wangler and Adebisi files a complaint against McManus with the Warden. Later, Oz is put on lockdown following a fight.
When Miguel's plea to return to solitary is ignored, he takes action in order to get what he wants. Glynn discovers who raped his daughter. The boxing finals take place, but the final match ends in tragedy.
Glynn receives a tempting offer from a gubernatorial candidate. Following a 24-hour lockdown, McManus struggles to get Em City back to its normal routine. Beecher asks his father to help Schilinger, despite him being his enemy. Meanwhile, Bellinger returns to Oz; Hamid Khan is taken off of live support, causing Cyril to struggle to deal with his guilt; and Arif requests Muslim leadership.
Glynn is forced to make a hard decision about McManus concerning his recent job performance hindered by his behavior. Dr. Nathan debates whether or not to have a meeting between her in-laws and the O'Reily brothers. Meanwhile, Alvarez survives a murder attempt; Beecher testifies; a juror in Cramer's trial comes forward to tell him the trial was not fair; and Mobay's cover is nearly blown.
Glynn discovers where Adebisi's gun originated from; Busmalis is sent back to Oz after stalking Whitney Allen; Mobay's cover is once again threatened when he has to decide between keeping his cover or taking drugs; the inmates win their civil cuit; Said helps Cramer start a motion for a new trial; and Schillinger has Hank kidnap Beecher's children.
Emerald City has a new Unit Manager who has an unusual approach to running things. Keller returns to Emerald City. Dr. Nathan confronts O'Reily about the attack. Meanwhile, McManus returns to Em City as the Unit B manager; Mobay and Busmalis are released from the hole; and the search for Alvarez continues.
Convicted detective Bruno Goergen arrives at Oz, which causes major problems for Mobay as he is forced to prove his legitimacy to Adebisi. Querns settles in to his new position as Unit Manager and moves Hoyt and the Bikers to Gen Pop. Meanwhile, new inmate Allah threatens Arif's status; Dr. Nathan's attacker is sent to Oz; and Zabitz reveals that Keller had Gary kidnap his children.
Said dishes out negative feedback to Querns, who later moves moves Keller out of Beecher's pod and replaces him with Browne. Officers Murphy, Mineo and Armstrong are relocated to Unit B as Officer Howell is transferred to Emerald City to address its diversity issue. Meanwhile, Beecher discovers who was behind the kidnapping; Ginzburg's execution date is moved up; Cyril overdoses on Haldol; and Ryan makes plans for Dr. Nathan's attacker.
Ryan O'Reily puts his plans in motion after a secret meeting with Claire Howell who takes care of Stanislofsky for him. Beecher goes after his children's kidnappers when Schillinger is freed on a technicality. Meanwhile, Rebadow is diagnosed with a brain tumor; Arif asks Said to take over the Muslims; Adebisi takes control of Em City as the gays, Italians and Hispanics are transferred to Unit B; and Governor Devlin is shot by Clayton Hughes.
Glynn pulls out of the gubernatorial race following the attack on Devlin. Hill accidentally tells Mobay that he knows about his secret, leading Mobay to turn himself in. Schillinger is visited by Hank's pregnant wife who is worried that Hank is gone missing. Querns is fired, which makes things look better for McManus. Said and Adebisi have a fight to the death.
Emerald City is shown to the world when news magazine producer Lisa Logan sends a camera crew to the block. While taping, she initially focuses on Beecher, but when she is given hints that there may be a cover-up concerning Adebisi's death, she changes her focus. But the focus is once again changed when Jack Eldridge has a reunion with the O'Reily brothers.
Alvarez is captured by police and brought back to Emerald City. After Dr. Nathan returns, she confesses her feelings toward Ryan to Sister Pete. Following the election, Devlin is inaugurated for his second term as governor. Meanwhile, Glynn's marriage ends; Busmalis proposes to Norma; Beecher gets a new podmate, who happens to have known Keller on the outside; new inmate Burr Reading arrives and takes control of the African-American drug scene; and Chinese refugees head to Emerald City's common room for shelter.
Alvarez gets himself out of solitary by becoming Glynn's informant. The inmates are able to receive reduced prison sentences by agreeing to test an experimental drug. Meanwhile, Giles is sent to death row; Busmalis receives permission to get married, but lands himself in the hole when his tunnel is uncovered; Hughes is transferred to Oz; and Barlog lands himself in a love triangle with Beecher and Keller.
After getting out of solitary, Alvarez finds himself back when he kills a Latino. Rebadow is able to convince Glynn to let Busmalis out of solitary. As the inmates continue with the drug testing, McManus lobbies against it and Cyril O'Reily begins to show the effects of the drug. The testing is immediately halted when Wick dies from blood running out of his mouth and nose. While trying to prove himself, Omar White stabs McManus. Meanwhile, Schillinger finds out that Hank is dead and Keller confesses that he ordered the hit on Hank, which sends him to Massachusetts for his trial.
Following Wick's death while taking part in the drug trials, his family sues the prison and Dr. Nathan is investigated for malpractice. Howell makes a play for Cyril that nearly lands him a transfer to the Conley Institute. Busmalis's wedding day is far from how he planned. Meanwhile, Beecher's parole is threatened; Shillinger meets his granddaughter; Giles chooses stoning as his method of execution; and Tidd is killed while protecting Said.
McManus tries to boost morale by starting a basketball tournament. Basil's wife is killed during a visit by Clayton Hughes who also stabs Yood. Jenkins confesses that he was hired by Robson to kill Said then later hangs himself. Meanwhile, Deyell dies during a failed escape attempt; a new inmate, Padraig Connolly arrives in Em City; and Cyril puts Jia Kenmin into a coma.
Beecher prepares for his parole hearing. Robson is released from solitary, but is brutally attacked by Said. Schillinger confronts his daughter-in-law about his granddaughter's paternity.
Supreme Allah sets out to kill Redding, but he finds Supreme Allah's one weakness. While in solitary, Hughes revs up a revolution, but is taken down when he tries to attack Glynn. McManus is beaten up by White after being ordered to solitary.
During the last year, a gas explosion damaged or destroyed most of the prison. Now, a year later, the inmates are able to return to Oz and are able to visit their loved ones for the first time in a long time. Meanwhile, Alvarez returns to solitary; Arif tells Glynn that Ryan O'Reily killed Kennan; and the bus transporting the visitors has an accident.
Montgomery tries to blackmail O'Reily, but his plan doesn't go as he had hoped. Brass returns to work in Emerald City as Suzanne Fitzgerald does her community service by teaching music to the prisoners. Meanwhile, Schibetta returns to Em City; Kirk orders Burns to kill Cloutier, but instead Cloutier has a vision that tells him to murder Kirk and Hoyt.
Morales and Alvarez reach an agreement, bringing a truce to their feud. As his grandson's condition worsens, Rebadow turns to his last resort to get the money to help him -- the lottery. Now out of the hole, Schillinger's first plan of action is seeking revenge on Pancamo. Schibetta tries to make a move on Schillinger, but gets raped in the process. Keller makes his return to Oz.
Inmates Hill, Alvarez and Penders are allowed to train seeing-eye dogs. McClain agrees to represent Keller, which adds to the complicated triangle between Beecher, McClain and Keller. Hill turns to drugs when he is unable to cope with his mother's death. Redding is put in control of the cafeteria.
Beecher grows suspicious of Schillinger's new found kindness. Said's sponsorship of White is damaged when Said learns he's dealing. Rebadow learns the results of the lottery. Kirk is transported back to Oz after his time at Benchley Memorial. Hoyt is moved to death row.
The Oz Variety show is held and Omar White has the honor of the finale. Cyril's trial begins, but gets off to a rocky start. Mukada convinces Hoyt to rat out Kirk. McClain walks out on Beecher and Keller.
Hill begins to recover from his drug-induced illness, which stirs up more friction between Redding and Morales. McManus finds a donor for Rebadow's grandson. Robson is removed from the Brotherhood following a rumor surrounding his gums. Meanwhile, Keller returns from Benchley.
Not wanting to be cast out of the Brotherhood, Robson removes his gums. White has to take extreme measures to prove his loyalty to Said. Busmalis learns that his former fiancee is pregnant. Beecher confesses to Sister Pete and Winthrop is sent to solitary. Cyril is transported to death row and Hill returns.
McManus comes across a box with Hill's memoirs of his past 6 years at Oz. Alvarez and Schillinger are transferred out of solitary to gen pop, and once Alvarez returns, McManus has him try to work things out with Guerra. Meanwhile, Rebadow gets some much needed cheering up when he is transferred to the library and meets Stella Coffo, the librarian; Kirk, who claims to be possessed, is transferred to death row; Suzanne Fitzgerald puts together an inmate production of Macbeth; Schibetta returns to Gen Pop; and Oz is placed on lockdown following race riots taking place outside of the prison.
As Beecher is granted parole, Mayor Wilson Loewen arrives at Oz, which, in turn, creates a twist in the feud between Schillinger and Beecher. The mystery behind why inmates in solitary confinement are getting sick is solved by Dr. Nathan.
Devlin scrambles to find a win-win solution to his pardoning issues when Loewen threatens to go to the press. Beecher says his goodbyes to Keller and is later released from Oz. Redding moves to telemarketing, opening up the kitchen, which Glynn gives to Pancamo. Meanwhile, Morales dies due to liver failure; Glynn learns why inmates are dying due to poisoning; Hoyt thinks he saw the devil while dealing with the guilt of killing Kirk; and Said is shot by a reporter.
An investigation into Said's death begins. Beecher uncovers more information about Keller's case, which leads to the overturning of Keller's sentence and he is returned to Unit B. Rebadow's relationship with the librarian becomes more complex when he learns she's sick. Meanwhile, Hoyt's sentence is overturned; new inmate Jahfree Neema arrives at Oz; White returns to Em City after making a deal with Glynn; and Dr. Nathan finds that Martinez was suffocated.
The Muslims put out the first copies of Hill's journal, but soon find that their business venture may not be as good as they had thought. Robson is able to rejoin the Brotherhood. Murphy goes to Glynn, which leads to the suspension of Brass. Busmalis is visited by Norma and the baby and she proposes to him. Meanwhile, Cyril's execution is rapidly approaching and he begins to show the side effects of ETC; Keller goes to Beecher for a favor, and then turns on him by ratting him out.
Omar White sponsors Idzik as he transfers to Em City. Glynn realizes a connection between Johnson and Loftus, which brings up more details surrounding Loewen's death. Robson continues with his rape counseling. The inmates support the O'Reilys as Cyril's execution nears.
New arrival Bukowski and his brownies infringes on the Italian's business. Busmalis and Norma tie the knot. Keller is once again caught in the middle of Schillinger and Beecher. Meanwhile, Seamus O'Reily arrives at Oz; Robson is given some bad news; and the Correctional Officer Association's annual awards banquet ends with a bang -- a surprise death.
Querns makes a return to Oz as a warden. As Howell learns that she's pregnant, Rebadow unsuccessfully petitions to artificially inseminate Norma. Vahue returns to Oz to talk to young prisoners and has a reunion with Brass. Alvarez receives bad news from the parole board. The mystery behind what really happened to Cloutier is revealed by Hoyt to Ray. Meanwhile, Idzik's death penalty sentence is overturned; Dr. Nathan lends her support to Ryan on the day of Cyril's execution; and the production of Macbeth is held, but Schillinger's fate is the same as the character he plays.