Beecher, an alcoholic lawyer, killed a young girl while driving drunk. Sentenced to prison, Beecher quickly learned that he was out of his element; his first week in the titular facility, he was raped by Vernon Schillinger, the leader of the Aryan Brotherhood, and was "branded" by having a swastika design burned into one of his buttocks. Beecher was regularly sexually humiliated by Schillinger and developed an addiction to heroin. He eventually snapped, attacking and humiliating Schillinger. Under the influence of PCP, he smashed the plexiglass wall of Schillinger's pod, sending a broken shard flying into Schillinger's eye. Beecher almost jumped to his death immediately after, but was restrained by guards and thrown in the hole. After being released, he confronted Schillinger (who was now sporting an eyepatch) in the prison gym's basketball court. He incapacitated Schillinger by hitting him in the groin with a piece of gym equipment, and continued to assault the Aryan in full view of the other prisoners, few of whom liked Schillinger and none of whom came to help him. Schillinger was beaten to the floor, where he had a bench slammed onto him and had his hands tied by Beecher, who proceeded to defecate on Schillinger's face. While this was cathartic for Beecher and was extremely entertaining to the others in the gym, it earned him another trip to the hole, which did nothing to improve his sanity.

When a riot erupted in Em City, Beecher sided with Ryan O'Reilly in the chaos. In the aftermath, Beecher and the other prisoners who'd been housed in Em City were sent to other sections of the prison. Beecher found himself sharing a cell with James Robson, who tried to make Beecher perform oral sex on him. The new, tougher, crazier Beecher wasn't having any of it and took Robson's penis in his mouth just long enough to bite part of it off and spit it out, sending Robson to the infirmary and Beecher to the hole once again.

Upon his release from the hole, Beecher began taunting and threatening Schillinger. However, Vern's parole hearing was coming up and he didn't want to get into trouble by becoming involved in a fight even if he wanted to tangle with Beecher again. Beecher continued to provoke Schillinger and succeeded in unnerving him, prompting him to look for other people to kill Beecher for him. Unfortunately for Schillinger, by this time Beecher had earned a reputation as a psychopath and none of the Aryans wanted to go near him. Schillinger began asking people outside the brotherhood to kill Beecher for him, but the ones who weren't afraid of Beecher hated Schillinger and wouldn't lift a finger to help him. Finally Schillinger seemed to find somebody willing to do the deed: guard Diane Wittlesey, whom he blackmailed with knowledge that she had shot a prisoner during the riot. Wittlesey reluctantly agreed to get rid of Beecher if Schillinger would keep quiet. Beecher disappeared and Schillinger subsequently met with Wittlesey to discuss their deal. During this meeting, however, Schillinger was under surveillance; Wittlesey had never intended to kill Beecher and had reported Schillinger's request to her superiors, who arranged to hide Beecher until they could get Schillinger on tape incriminating himself. Schillinger obliged them, and Beecher had the satisfaction of being present to see the look on his face when he realized what had happened. Afterwards, with Schillinger in the hole, Beecher bragged to his new cellmate Augustus Hill that even though he was crazy, his plan had worked perfectly. He'd been able to push Schillinger into doing something reckless and now, as a result, Schillinger would be charged with conspiracy to commit murder and had no chance at parole. Hill warned him that Schillinger would be out for revenge and now had less to lose than before, but at the moment Beecher was too happy to care.

Beecher was then moved to a new pod with a new cellmate, Chris Keller. Initially Beecher was uninterested in getting to know Keller. This changed after he saw Keller being bullied by some Aryans, whom Beecher helped fight off, and after Keller showed him sympathy and friendship. Beecher was surprised to find himself becoming attracted to Keller. Unfortunately, Keller was working with Schillinger, in order to help the latter get revenge on Beecher. After using Beecher's attraction to Keller to put him through an emotional ringer and start him drinking again, the two cornered a partially drunk Beecher with the help of an Aryan guard and broke his arms and legs.

Keller discovered that he had genuinely fallen in love with Beecher, however, and was desperate to win Beecher's trust and love again after he recovered. Though Beecher was initially skeptical, Keller's abandonment of Schillinger and the Aryans and his aid of Beecher and Ryan O'Reilly in their joint effort to get revenge against Schillinger (who had raped Ryan's mentally retarded brother Cyril) convinced Beecher of his sincerity. But Beecher would not be ready to forgive Keller for a long time. This was no more evident than when Beecher ambushed Keller shortly after his release from the infirmary, stabbing him. Although Keller never saw his attacker, Beecher told him that he'd been the one who attacked him some time later. Beecher finally forgave Keller after he saved his life.

The conflict between Beecher and Schillinger continued throughout the run of the series. When Schillinger's son Andy was arrested and incarcerated in Oz, Beecher saw his chance to get even with Schillinger by befriending Andy and arranging to share a cell with him. While Beecher never did anything bad to Vern's son and in fact helped Andy cope with his withdrawal from drugs, he led Vern to believe that he was going to make Andy his prag in order to torture Vern psychologically. Vern was scared to death about what Beecher would do to his son, and in the end Andy renounced his father and the Aryan way of life after realizing (in part due to his interaction with Beecher) how screwed up it was. Vern felt that he had no alternatively but to have Andy killed, a decision which he felt terrible about despite believing it was necessary. Beecher's co-conspirators in the plan (Keller and Ryan O'Reilly) were happy about the outcome, since they had tormented Vern and turned his son against him. Beecher wasn't as satisfied, despite having gotten revenge.

In retalation for what happened with Andy, Vern had his other son, Hank, kidnap both of Beecher's children and kill one of them before ultimately releasing his daughter. Hank Schillinger severed the hand of Beecher's son before killing him and mailed it to Beecher in Oz, traumatizing Beecher immensely. Vern Schillinger also paid another prisoner to tell Beecher that Keller was responsible for the kidnapping, resulting in Beecher trying to murder Keller and a falling out between the two lovers. When Beecher learned the truth, he approached Chucky Pancamo in order to commission a mob hit on Hank Schillinger. Beecher had second thoughts about this shortly after, but when he went to Pancamo to cancel the hit he was informed that it was too late; Hank Schillinger was already dead.

Over the course of his imprisonment, Beecher developed a close friendship with fellow inmate Kareem Said and engaged in a tortured love affair with Keller. While in prison, Beecher struggled with his addictions, his sexuality, and his culpability in the various crimes he had committed.

Beecher was paroled, but was sent back to prison after a lonely Keller arranged for him to get caught buying illegal drugs. Keller had told Beecher that his ex-wife was terribly ill and asked Beecher to pick up a drug for her that hadn't been approved by the F.D.A. and was thus illegal. After Beecher agreed to do so, Keller anonymously telephoned the police and told them where the deal would take place. Once in prison again, Beecher renewed his war with Schillinger and banished Keller from his life. Attempting to make Beecher forgive him, Keller engineered Schillinger's death; during Oz's production of Macbeth (in which both Beecher and Schillinger had been cast), he switched a prop knife for a real one, resulting in Schillinger's death when Beecher stabbed him. Once Beecher realized what had happened, he and Keller got into a heated argument which ended with Keller killing himself by throwing himself over a railing to make it look like Beecher killed him. The fall broke Keller's neck. At the time of the anthrax attack at the end of the series, he was in protective custody to shield him from the other Aryans, and awaiting trial for Keller's death, although staff psychiatrist "Sister Pete" believed that he would be exonerated.