Talk to Alex and tell him to reveal what he's lying about. He will explain his situation.
Allow Alex to tag along. During the Gauntlet, ensure to engage mutants at maximum range and kill ones that threaten him first to prevent him from dying an ignoble death.
Enter the Penitent Barracks and talk to Luis. He will berate the Rangers and refuse to leave until the player finds a way to free all of the penitents.
Once the Rangers install Ascension McDade as leader and start forging a peace between the Bastion and Hollywood, Retribution Jones will rebel. Killing him and wiping out his supporters outside the Bastion will allow the Rangers to talk to Luis and free the penitents.