During the siege, Vargas, along with many others in the contingent, suffered deep psychological trauma. Vargas in particular suffered over the death of McGreevey even though he had not liked the man.
When Sisko along with other members of Deep Space Nine arrived on the planet to help defend AR-558, Vargas mistakenly fired on them. Along with the crewmembers from Deep Space 9, Vargas and the rest of his squad were able to hold their ground during a final attempt by the Jem'Hadar to recapture the planet. Vargas, however, was stabbed in the back and killed during this attempt.