Tobias Beecher wanted to make peace with Vern Schillinger, and Keller was against this. He and Keller had been lovers for a while now. Beecher then asked his father to locate Schillinger's other son, Hank. When he informed Keller, Keller called him his "bitch". Beecher, refusing to be anyone's bitch, punched him and spent some time in the Hole. The day he returned, an inmate when on a shooting spree that hit Keller in the chest. Beecher dragged Keller to safety.
[Episode 25: "A Cock and Balls Story"]

He was worried about Keller, and nobody would give him an answer on Keller's condition.
[Episode 26: "Obituaries"]

Keller met with Father Ray Mukada in the hospital ward, explaining that he'd died on the operating table twice and wants Sister Peter-Marie to forgive him for fucking with her. Sister Pete refused to even see him.
[Episode 27: "The Bill of Wrongs"]

Keller returned to Emerald City to a depressed Beecher, for someone had kidnapped Beecher's children. Later, Keller was crying and he woke up Beecher, saying that he'd died and gone to hell and it scares him. Beecher received a package containing his son's hand, and Keller couldn't be very comforting to Beecher anymore.
[Episode 28: "Works of Mercy"]

Beecher, while preparing for his son's funeral, revealed to Keller that he knows Keller is suspected in the murders of several homosexual men and wants to know if he is the first man Keller's felt this way about. Keller claimed he was, but Beecher believed he was lying. Later, Keller offered to help Beecher find and kill the man who killed his son, and Beecher attacked Keller with a shank, screaming that Keller murdered his son. Keller was dragged to the Hole.
[Episode 29: "Gray Matter"]

When the real killer of Beecher's son was found (Hank Schillinger, the son that Beecher had payed to have found), Keller returned to Emerald City. He was placed in a cell with Liam Meaney, and broke up with Beecher right away. Keller approached Schillinger, gloating that he's killed his sons. He went to confessional with Mukada, claiming that he killed several men on the outside. Mukada refused to give him his penance if he doesn't confess. Late one night, Keller watched Beecher have sex with his new cellmate, Mondo Browne.
[Episode 30: "A Word to the Wise"]

Keller learned that inmate Eli Zabitz had lied to Beecher and said that Keller had had his children abducted. Keller approached Zabitz and subtlely threatened to kill him. When Keller (and Jim Robson, for other reasons) cornered Zabitz to kill him, Zabitz died of a heart attack. Father Mukada tried to convince Keller to forgive Beecher, but Keller refused. Later, Keller and Ryan O'Reilly saw that Emerald City was getting more and more black inmates.
[Episode 31: "A Town Without Pity"]

Sister Pete came to Keller, explaining that "we don't choose God, God choose us". Keller believed this to be bullshit, and turned his back on Catholicism. Keller and Ryan decided to do something to bring down the black utopia of Emerald City. Keller killed Nate Shyamen, a man that Beecher had slept with. He then found Beecher searching his stuff, and Beecher claimed that he plans on turning Keller in for killing Shyamen. Keller believed that Beecher'd had Schillinger's son killed and planned to use this if Beecher turns him in. Then Keller killed Browne and planted evidence implicating Supreme Allah.
[Episode 32: "You Bet Your Life"]

He was interviewed by reporters about his relationships with Chris Keller and Vern Schillinger.
[Episode 33: "Medium Rare"]

Ronald Barlog (Keller's old friend) was sent to Emerald City, and became Beecher's cellmate.
[Episode 34: "Conversions"]

Beecher used Barlog to get back at Keller, but Keller had the last laugh when Barlog became his new boyfriend. Beecher learned that Barlog was planning to sell Keller out to the FBI and warned him, so Keller killed Barlog, and peace was declared between Beecher and Keller again.
[Episode 35: "Revenge Is Sweet"]

When Hank's body was found, Schillinger decided to kill Beecher's entire family. To save Beecher and his family, Keller confessed to the murder and was transferred to Massachussettes.
[Episode 36: "Cuts Like A Knife"]

Beecher learned from his lawyer, Catherine McCain, that his parole was approaching.
[Episode 37: "Blizzard of '01"]

He called Keller and excitedly told him, but Keller told him to forget about him.
[Episode 38: "Orpheus Descending"]

Beecher met with his original victim's family in preparation for his parole hearing. He also began to get a lot closer to his lawyer, Catherine.
[Episode 39: "Even the Score"]

Schillinger planned to ruin Beecher's parole, but didn't need to, as the parole board turned him down anyway. When Schillinger and Robson threatened Beecher in the library, Kareem Said stabbed them both to save Beecher.
[Episode 40: "...Famous Last Words"]