McManus was excited for his girlfriend, Diane, to return from her vacation in England. Then Sister Peter-Marie informed him that Diane had met a guard and was getting married to him. McManus began to drink. Inmate Guillaume Tarrant came to McManus, crying because Kenny Wangler stole his shoes. McManus told Tarrant to give him evidence that can implicate Kenny. Soon afterward, Tarrant went on a shooting spree and shot Officer Joe Howard right in front of McManus. Then Tarrant killed himself.
[Episode 25: "A Cock and Balls Story"]

After the shooting, McManus sang a song at Howard's funeral that was about gambling but racially degrading, so McManus was fired from Emerald City.
[Episode 26: "Obituaries"]

After seeing an affordable psychiatrist, McManus came to Glynn, begging for his job back. Glynn explained that he'd already hired someone to run Emerald City, but offered Unit B. McManus agreed to take it.
[Episode 28: "Works of Mercy"]

McManus received a call from Diane, wanting to talk to him. Instead, he hung up on her.
[Episode 29: "Gray Matter"]

Officer Sean Murphy complained to McManus that Martin Querns, the new guy running Em City, has transferred the white officers out and is bringing black men in. McManus gave his old friends a job in Unit B and complained to Glynn. Glynn explained that Querns's system is keeping the violence down, but McManus was skeptical. Then Officer Claire Howell informed McManus and Murphy that she was now working in Em City.
[Episode 30: "A Word to the Wise"]

Vern Schillinger came to McManus, explaining that Emerald City is an almost all-black unit, and suggesting that McManus make Unit B an all-white unit. McManus yelled at him and locked the unit down. He then complained to Glynn that Em City is a mess, but Glynn still wouldn't listen. Later, Kareem Said approached McManus with a plan of bringing down Querns.
[Episode 31: "A Town Without Pity"]

Said gave McManus a tape of inmates using drugs, and McManus gave it to Glynn. Glynn watched the tape and fired Querns, then offered McManus his job back. McManus took it back and began to clean up Querns' mess.
[Episode 32: "You Bet Your Life"]

He was investigated by reporters during their filming of a documentary. He fingered his predecessor, Martin Querns, as the man responsible.
[Episode 33: "Medium Rare"]

In his ongoing crusade to improve the quality of inmates' lives, he implimented a cage that inmates will stay in if they get into trouble. He also was forced to house Chinese refugees in his unit, and one claimed that inmate Burr Redding had threatened him. McManus warned Redding, but the man ended up dead anyway. McManus put Redding into the cage.
[Episode 34: "Conversions"]

Having had no real evidence ("except the word of a dead man"), McManus was forced to drop the charges against Redding.
[Episode 35: "Revenge Is Sweet"]

A drugged-out inmate named Omar White stabbed McManus in the middle of Emerald City.
[Episode 36: "Cuts Like A Knife"]

When McManus returned from the hospital, he learned that Oz was in lock-down because of a war between the Homeboys, Sicilians, and Latinos. He forced Redding and Enrique Morales to make peace, ending the lock-down. He also made a note to forgive White and let him back into Em City. He later saw Jackson Vayhew shooting hoops in the gym, and the two exchanged male insults, and finally they challenged each other to a three-game torunament between the inmates and officers. In the first game, Vayhew and teammate Agamemnan Busmalis beat McManus and Officer Brass.
[Episode 38: "Orpheus Descending"]

White got into a fight during drug rehab, and Sister Peter-Marie gave up on him. McManus vowed that he wouldn't. To make Brass play better, McManus got a professional scout to watch the second game. The officers won, and Brass was told that he might be accepted into a professional team. McManus told Brass that he doesn't have to play in the final game. Later, Morales bragged to McManus that he will lose without Brass, so McManus (to wipe the smug grin off his face) told him that Brass is still playing. Soon afterward, an unidentified inmate slashed Brass' ankle, debilitating him.
[Episode 39: "Even the Score"]

For the third and final game, McManus' teammate was Officer Murphy. They lost to Vayhew and Busmalis. White began to follow McManus around like a two-year-old. When McManus appeared on a TV show (and lost!) and the Latinos made fun of him, White killed one, and McManus was forced to send White to Solitary, and White kicked the crap out of him. Stubborn ol' McManus still refused to give up on him.
[Episode 40: "...Famous Last Words"]