After getting his arms and legs broken, Beecher returned to Emerald City with a beard, long nails, and walking with a cane. His cellmate, Chris Keller, tried to apologize for breaking his limbs, but Beecher cooly told him off while filing his nails. He convinced Keller that the road to salvation was confession, so keller immediately confessed everything. Then Officer Karl Metzger, nervous about what Keller may be confessing, pulled Beecher into a dark hallway with the intention of beating the news out of him. Beecher got back at Metzger by using his newly-sharpened nails to slash and slice Metzger's face and throat. Metzger bled to death while Beecher clipped his nails.
[Episode 17: "The Truth and Nothing But..."]

Keller wanted to kiss Beecher, but Beecher rejected him. Keller yelled at him, saying that he's given up so much because of him. Beecher still believed that this may be a scheme of theirs, and that he cannot trust him anymore.
[Episode 18: "Napoleon's Boney Parts"]

Keller offered to help Beecher get back at Schillinger, but Beecher refused his help, citing Metzger's murder as an example of how he can handle himself. He prayed for a way to "fuck Schillinger", and the next day young Andrew Schillinger came to Emerald City.
[Episode 19: "Legs"]

Keller and Ryan O'Reilly sought a way to use Andrew to get Schillinger, and Beecher developed a plan. He stood up for Andrew in rehab group, and later told a sob story to Tim McManus about how he feels sorry for Andrew and can help him. McManus let Andrew become Beecher's cellmate. They shared tatoos and hit it off quickly.
[Episode 20: "Unnatural Causes"]

Andrew soon went through withdrawals, and Beecher helped him through it. Andrew and he became buddies. However, Beecher taunted Schillinger with this, saying that he may take advantage of the boy soon. Andrew stood up to his father for his friends, which resulted in Andrew ending up in the Hole. His body was found soon after, and Beecher regretted his part in the boy's death.
[Episode 21: "U.S. Male"]

Keller tried to get back into Beecher's cell but Beecher turned him down. Beecher went to Kareem Said and asked him about Allah and Islam, and Said invited him to listen to the Muslims' discussion group. This choice made the other Muslims cast Said out. Beecher asked Said to continue to teach him, and Said became his new cellmate.
[Episode 22: "Cruel and Unusual Punishment"]

Beecher prayed like a Muslim with Said, but continued to reject Keller. Said taught him that forgiveness leads to redemption, so Beecher forgave Keller. When he went to forgive Schillinger, Schillinger himself stabbed Beecher. Keller stabbed Schillinger and cradled Beecher until help arrived.
[Episode 23: "Secret Identities"]

When Beecher returned from the hospital, he was so grateful to Keller that he let Keller become his cellmate again. The two made out when the clock struck midnight on New Year's 1999-2000.
[Episode 24: "Out of Time"]