When Morales is killed, Guerra wants Alvarez to lead the Latinos although Guerra is tiring of all the violence over the past years. Guerra is ordered to kill a stricken Martinez. Morales believes that Martinez told the CO's that Morales ordered Officer Brass' ankle cut. Guerra goes to do the job but changes his mind after an ill Martinez tells Guerra that he's too weak to defend himself. New inmate Torquemada arrives an introduces a new drug, 'D' to all willing inmates. Guerra starts using the drug which gives the user feeling of unbelievable energy and power. However, Guerra has taken taken so much 'D' that he lapses into a hallucenogenic fit in the laundry room and tries to scratch his skin off. He's then carted away to the hospital for an indefinite stay.
This season, Guerra's priority was to get revenge on Alvarez for killing Vasquez. Alvarez knows this and presents Guerra with an unusual offer--Guerra can stab Alvarez in front of all the inmates only the stabbing cannot be fatal. Guerra and Alvarez go through with the deed and Morales announces that their beef is squashed and no more acts of vengeance will happen. What Guerra doesn't know is that after he shanks Alvarez, a young Latino inmate sees this and decides to follow Miguel. Miguel orders this young inmate to kill Guerra. He goes to do the deed only Guerra turns the tables and kills the guy by bashing his head into the shower stall wall.
Season 4 Part 2
Continues being Morales' right hand and gets an order from Morales to have Alvarez killed. Guerra goes to Omar White to ask him for the deed only Omar refuses. When Guerra challenges White on this, White shanks him. As revenge, Guerra tells McManus that White's still using drugs which results in Guerra getting thrown in the cage and White getting yelled at McManus.
Season 4 Part 1
Morales arrives and immediately plans to take control of the Latinos from Hernandez. Guerra of course moves his allegiance from Hernandez to Morales and vows to help him.
While Hernandez tells O'Reily to stop selling drugs, Guerra's along as muscle. However, O'Reily turns the tables by ratting to the guards that the Latinos are holding. This results in Guerra getting put in solitary with all the Latinos, except Alvarez. Hernandez suspects Alvarez's complicity tells Guerra to hurry and kill Alvarez. Guerra and Ricardo go to do the deed only Alvarez kills Ricardo. Once more, Guerra and Hernandez are left planning on how kill Alvarez. When the boxing matches begin, Guerra supports Hernandez in their manipulation of Alvarez.
When El Cid (Hernandez) arrives, all the Latinos, including Guerra throw their support behind him. Follows Hernandez's lead in ostracizing Alvarez.
With Alvarez as their leader, Guerra keeps wanting to make a move against other groups for total control of the drug trade. Alvarez warns him to be patient because a plan is brewing.