New officer Claire Howell asked McManus out on a date. With an attack on Agamemnan Busmalis, McManus believed that his supervising officer, Karl Metzger, was untrustworthy. He asked Busmalis and Tobias Beecher to testify against Metzger, but neither would. Soon afterward, Chris Keller came to McManus and explained that he, Vern Schillinger, and Metzger had attacked Beecher. Metzger's body was found soon after.
[Episode 17: "The Truth and Nothing But..."]

McManus decided to bring in an old friend who works at Attica named Sean Murphy to be the new supervisor. He also asked Murphy to help him organize a boxing tournament in Oz to help keep things down. McManus later came to Diane Whittlesy (his ex-girlfriend) and Howell and informed Diane that her mother had died. Diane cried, and McManus held her. Later, Howell attacked McManus out of jealousy.
[Episode 18: "Napoleon's Boney Parts"]

Howell came to McManus, apologizing for their fight and wanting them to still have sex. McManus turned her down, and Howell attacked him again. This time inmates witnessed it. Howell stormed away and ended up beating an inmate in Solitary badly. McManus demanded that Warden Glynn fire Howell, which Glynn did.
[Episode 19: "Legs"]

Glynn informed McManus that Howell is suing him for sexual harassment. McManus had a meeting with Howell's attorney and the state's attorney. McManus explained everything, but the state decided to believe Howell's side and give her her job back. McManus ran into her in the locker room, and she told him that if he says one word to her, she'll scream.
[Episode 20: "Unnatural Causes"]

McManus had to inform inmate Kenny Wangler that his wife had been found dead with a lover, but his baby was OK. He also decided to counter-sue Howell, but after talking to Gloria Nathan he decided against it. He instead talked to Diane and asked her if she would've helped him. She said yes, because what they'd had was real.
[Episode 21: "U.S. Male"]

McManus decided to help counsel Kenny and make him a part of his son's life.
[Episode 22: "Cruel and Unusual Punishment"]

Kenny went to Glynn and claimed that McManus had fondled him. McManus got even more stressed, and soon afterward TV cameras interviewed Kenny and Howell, but McManus chased them out of his office. He heard that Diane had been smacked in the head and went to see her. He confessed that he sometimes thinks of starting things up between them, and she kissed him as Howell walked by.
[Episode 23: "Secret Identities"]

While McManus ate lunch with Diane and explained his troubles (the sexual harassment things), Howell walked by and Diane punched her. Glynn yelled at McManus for these two women fighting over him, and everyone in the hospital heard. As racial tensions in Oz grew, Diane confessed to McManus that she will take her vacation time or quit. Murphy and McManus also discussed what to do to make tensions lower.
[Episode 24: "Out of Time"]