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When Warden Glynn's daughter was raped by a group of Latinos, the Warden took out his frustration on Alvarez. Alvarez learned the identity of the rapist and his bragging was overheard by Richard Hanlon who told the Warden. The Warden and Alvarez ended up having a punch out and Alvarez was put in the hole. Alvarez received offers from Peter Schibetta to kill Adebisi, and offers from Adebisi to kill Schibetta- he declined both offers. Miguel lost his place as leader of The Latinos to El Cid, who rejected Alvarez as a Latino saying Miguel is "too white". El Cid started calling Alvarez "Michael" (English for Miguel). Alvarez asked El Cid what he can do to prove himself to him and El Cid told Miguel to take out the eyes of a C.O who was a former member of a rival gang. Miguel tossed the issue around for quite some time and found it to be no-win situation. If he takes out Officer Rivera's eyes, the hacks are gonna beat him down and put him in solitary confinement, and if he doesn't do it, El Cid is gonna kill him. Miguel finally cut out Rivera's eyes and hid in Father Mukada's office. The hacks eventually found Miguel, beat him down, and put him in soliatary confinement...possibly for the remainder of his life.
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Since Alvarez plucked out a C.O's eyes, the other C.Os "forget" to feed him. Alvarez has been living on his own piss and excrement. The prison hospital is now owned by Weigert;a company that wants to cut down on excess treatment so they won't allow Dr. Nathan to provide Alvarez with anti-depressants anymore even though she explained Miguel is a threat to himself. Father Mukada tried to sneak Miguel a peanut butter and jelly sandwich and was attacked by Miguel. The C.Os beat Miguel badly. Miguel made his shirt into a noose and hanged himself. Dr. Nathan was able to save Miguel's life, and Miguel was very disappointed when he found out he wasn't dead. Miguel cut a deal with the Warden to get out of Solitary if he told him who raped his daughter. El Cid still wanted Alvarez dead so he sent Chico Guerra and Carlo Ricardo on him. Miguel was sent back to Solitary and then told him Carlo Ricardo raped his daughter. -----
Miguel told Luis Bevilaqua that he had killed Carlo Ricardo during an experiment called soliatry rec-time were the inmates in solitary would walk around the gym in a circle chained to eachother. It was than revealed that Bevilaqua was the person who actually raped the Warden's daughter. El Cid gave Bevilaqua the OK to kill Alvarez. William Giles was behind Bevilaqua and saw the weapon his had in his waist an pulld it out and killed Bevilaqua and stabbed Alvarez. El Cid ordered Carlos Martinez to kill him in the hospital. Miguel was able to stop Martinez' attempt. While in the hospital Miguel convinced "The Mole" to let him escape with him and Miguel was on the run for all of Season 4 Part 1
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Miguel was found and was brought back to Soliatary. Miguel cut yet another deal with the Warden to get out of Solitary. Alvarez agreed to be the Warden's eyes and ears in Em City, but the Warden wasn't impressed with his ork and the only way Enrique Morales would let him back into the gang was if Alvarez killed Burr Redding. Miguel got into a fight with another Latino and slit his throat and ended up back in Solitary.
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During the reconstruction of the kichen, it was discovered that there was a problem in the air ducts in Solitary so all the inmates had to be removed and they were also given a second chance, if they didn't get into any trouble they wouldn't have to return to Solitary. Miguel got in every Latino's face and showed everybody that he didn't care and he wasn't afraid of anything. Miguel told Guerra that he would let him stab him in the shoulder in he squased the beef between them. Guerra stabbed Miguel but he tried to go for the heart. Alvarez survived and was then being protected by Morales because Morales was concerned about Alvarez for some reason. Alvarez became involved in a program where inmates train seeing eye dogs. Miguel was the only inmate successful and he gave the dog to the C.O that he blinded.