Alvarez has been in Solitary Confinement for months now. Doctor Gloria Nathan informed him that he is being cut off from his anti-depressants. Father Ray Mukada came to see Alvarez, and Alvarez admitted to him that the officers "forget" to feed him.
[Episode 17: "The Truth and Nothing But..."]

Alvarez's depression spiraled deeper and deeper, until finally he hung himself in his cell.
[Episode 18: "Napoleon's Boney Parts"]

Officer Howell discovered Alvarez hanging and had him sent to the hospital, where Nathan revived him. When he awoke, he told them that they should have let him die.
[Episode 19: "Legs"]

Sister Peter-Marie came to Solitary Confinement and introduced the idea of a victim-offender interaction program to Alvarez, telling him that if he participates, he can be moved out of Solitary for the duration of the program. But in return, he must tell Warden Glynn who raped his daughter. Alvarez returned to Emerald City, and Raoul Hernandez and Carmen Guerra asked him to be their boxer, because Carlos Ricardo was supposed to do it, and he's in the Hole. Alvarez boxed Jason Cramer and lost.
[Episode 20: "Unnatural Causes"]

Alvarez revealed to Sister Pete exactly how he blinded Eugene Rivera.
[Episode 21: "U.S. Male"]

The El Norte members forced Ryan O'Reilly to stop selling drugs, and Ryan turned them in. Alvarez saw the officers coming and walked away, but Hernandez, Guerra, and Ricardo were arrested.
[Episode 22: "Cruel and Unusual Punishment"]

Sister Pete took Alvarez to meet Tina and Eugene Rivera. Rivera asked Alvarez why he did it, and Alvarez told him. Then Alvarez asked for their forgiveness, and Rivera refused to give it.
[Episode 23: "Secret Identities"]

Hernandez, Ricardo, and Guerra were released from Warden Glynn's custody, and they were really mad at Alvarez and decided to kick him out of El Norte. Sister Pete informed Alvarez that Rivera doesn't want to continue with the program, so Alvarez will have to return to Solitary if he doesn't tell Glynn who raped his daughter. Alvarez still refused to tell. As he was packing his stuff, Ricardo and Guerra tried to kill him. Alvarez stabbed Ricardo in the stomach, and held a knife to Guerra's throat. He surrendered when the officers arrived, and Officer Mineo announced that Ricardo is dead. Alvarez was thrown into Solitary once again. That night, Glynn came to Solitary to talk to Alvarez, and Alvarez finally confessed that Carlos Ricardo had been the one who raped Glynn's daughter.
[Episode 24: "Out of Time"]