In 2375, during the Dominion War, he was assigned to AR-558, a planet that the Federation Alliance had captured from the Dominion. His commanding officers were Captain Loomis and Commander Parker. Fellow members of his unit included Reese, Crewman Kellin and Nadia Larkin.
Five months later, the majority of the original personnel assigned to protect the planet's communication array were dead, including Loomis and Parker. Larkin now commanded the troops.
When Sisko along with other members of Deep Space 9 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. (DS9: "The Siege of AR-558")