1997

He was sent to Oz, and asked by Nino Schibetta to look for the killer of Dino Ortolani. O'Reilly turned in Johnny Pose, and then he arranged to have Jefferson Keane killed. When he got Officer Mike Healey fired, he quit doing drugs, but he continued to sell them. He and Simon Adebisi slowly killed Schibetta.

1998

O'Reilly was diagnosed with breast cancer, and underwent an operation. He survived, and fell in love with Doctor Gloria Nathan, the surgeon who saved his life. He divorced his wife, Shannen, and had his mentally-retarded brother Cyril kill Nathan's husband. Cyril confessed to the murder, and was sent to Oz. O'Reilly confessed to the murder to help protect Cyril.

1999

O'Reilly tried to get Jazz Hoyt to kill Vern Schillinger for raping Cyril, but the plan didn't work. When an Oz boxing championship started, O'Reilly signed Cyril up. He also began to drug the water of the men Cyril boxed so Cyril would win. Cyril got to the championship boxing match against Hamid Kahn, and told Cyril to picture Kahn as their father. Cyril beat Kahn so badly, he became brainded. Cyril beat up O'Reilly out of anger.

2000

To help calm Cyril down, O'Reilly signed he and Cyril up for meeting Nathan. That didn't go well, and O'Reilly learned that Nathan was raped recently. To make Nathan feel better, he confessed to the raping. The real rapist, Patrick Keenan, was sent to Oz, and O'Reilly murdered him. O'Reilly discovered that Nikolai Stanoslavski had a cell phone, and Nikokai agreed to share with O'Reilly. O'Reilly got Hoyt to attack Nikolai, and in the fight O'Reilly got ahold of the cell phone. Nikolai cleverly got the cell phone taken away from O'Reilly. O'Reilly had sex with Officer Claire Howell so she would kill Nikolai, which she did. But when he tried to break off their relationship, she forced him to keep having sex with her.

2001

When a news crew wanted to make a documentary on Oz, O'Reilly recognized the reporter, Jack Eldridge, as the man who'd ruined he and Cyril's reputation when they were teens. He wanetd to get new arrival Omar White to hurt Eldridge, but it backfired when White was sent to Solitary, and Cyril ended up beating Eldridge. O'Reilly finally convinced Howell to leave him alone, but she began to make moves on Cyril. Cyril beat up inmate Jia Kenmin and put him in a coma, and was almost sent away. O'Reilly confessed to Nathan that he had killed Keenan, and she began to fall in love with him as well. She helped Cyril get returned to Emerald City. A woman named Suzanne Fitzgerald visited O'Reilly, claiming to be his real mother and that he and Cyril were half-brothers. O'Reilly developed a relationship, and she confessed that she had committed a murder in the '60's and was going to turn herself in. Inmate Jia Kenmin picked a fight with Ryan, and Cyril knocked Jia into a coma. Irish terrorist Poraig Connelly was sent to Emerald City and he and O'Reilly constructed a bomb to blow up Em City. O'Reilly's conscience kicked in at the last minute, and Emerald City was saved from Connelly's bomb.

2002

Zahir Arif confessed to Warden Glynn that he had seen O'Reilly kill Keenan and take a necklace from him. After Glynn questioned O'Reilly, O'Reilly then tried to set up the murder on Henry Stanton (an inmate who was trying to befriend Cyril), then had the necklace placed in the cell of Martin Montgomery (the man O'Reilly had paid to say he'd seen Stanton kill Keenan). When Montgomery tried to blackmail O'Reilly, O'Reilly manipulated Henry into attacking and stabbing Montgomery. Soon afterward, O'Reilly's mother Suzanne returned to Oz to work her two years of community service there as a music teacher. Recovered Jia returned and made peace with Ryan and Cyril. Later, he and Glen Shupe told Ryan that inmate Li Chin planned to rape Suzanne, so Ryan attacked Li with a shank. It was Cyril who stabbed Li to death. Cyril was sentenced to death, and transferred to death row. Ryan's new cellmate, Father Meehan, offered to help save Cyril. Ryan at first refused, believing that the best thing that could be done for Cyril was to let him die. Meehan tried to save Cyril anyway, and Ryan eventually changed his mind and offered to help.

2003

Meehan and Ryan did their best to try and save Cyril, and also participated in Suzanne's production of "Macbeth" by Ryan painting the sets and Meehan playing Macbeth. However, Ryan discovered Meehan's body in their cell, dead of an aneurism. Later, Peter Schibetta told Ryan that he knows Ryan killed his father back in 1997. Ryan ran into Peter Schibetta in the gym, where Peter revealed that he had given Father Meehan the "evil eye" curse the day he'd died (basically, the "evil eye" is when someone steals something of someone's and uses it to poison the person's body). Peter planned to curse everybody close to Ryan, and then Ryan himself. Ryan tried to warn Suzanne. She was skeptical, and then noticed that her car keys were missing. Ryan went straight to Chucky Pancamo and asked him about the "evil eye" curse. When Pancamo admitted that it is a legitimate thing, Ryan told him that Peter was planning to curse both Ryan and Pancamo. At count that night, Peter was dead, and Pancamo gave Ryan his mother's car keys back. Sister Pete informed Suzanne and Ryan that the circumstances had been set so that they would have no say in what happens to Cyril, and that Cyril would undergo electro shock therapy. Cyril began undergoing ECT, and afterwards was drooling and disoriented when Suzanne and Ryan came to see him. When Jazz Hoyt's death sentence was overturned, Ryan was pissed that the state values Hoyt's life over his brother Cyril's. Suzanne informed him that she'd had a fling with Emerald City's newest arrival, a former Black Panther named Jahfree Neema. Ryan spoke to Suzanne, upset that she'd been involved with Neema. He was also pissed that Cyril's appeal had been denied. Their attorney was going to appeal to the State Supreme Court, but he doubted it would do any good since Cyril's execution is scheduled for next week. Ryan and Nathan discussed Cyril's upcoming execution. He wanted Cyril to have lethal injection, but Nathan suggested that it may be easier on Cyril if they give him the electric chair (he'd been having electro shock therapy anyway). Ryan spoke to Cyril that he was going to have "one more special ECT treatment" and he'd be able to have anything he wants for dinner, and that Ryan would be able to be with him. Cyril was ecstatic, even though Ryan told him he'd have to lose his hair. At the barber shop, Cyril's head was shaved bald. As Ryan sat in Emerald City, Jahfree Neema told Ryan that he respected what he's been doing trying to save Cyril and told him that he's arranged something for when Cyril's hour arrives. Ryan spent the night with Cyril in his death row cell. An officer kept writing a report, and Ryan paid the man for a copy. Suzanne came to Cyril and taught him a special prayer before she and Ryan were kicked out of death row. Cyril was given his favorite of Ryan's shirts to wear. Ryan asked McManus if he can walk around his special maze when Cyril's time comes. As Cyril was being lead to the chair, Neema stood up. Ryan, McManus, and Murphy watched as all inmates of Emerald City entered their cells and began to pound on the glass. Murphy led Ryan to the gym and let him wander the maze. Cyril was strapped to the electric chair, and when Glynn told him he can make any last statement he likes, Cyril chose: "Huh?" Sister Pete held Suzanne's hand as the men began to charge the chair. Ryan cradled the Bible as he prayed. Glynn's phone rang, and after he hung up he announced that the state supreme court has issued a Stay of Execution for Cyril for the immediate future. That night, Ryan held the Bible in one hand and was reading the officer's report, and he just said, "Thank you" over and over. Ryan was happy that Cyril wasn't going to die, even after Suzanne reminded him that Cyril's death sentence hadn't been overturned, just postponed. Ryan met with Nathan, asking her if he can work in the hospital to help others survive. She agreed. When Ryan heard that his father, Seamus, was coming to Oz, he went to McManus and demanded that Seamus not come to Emerald City.