Ayala was a Maquis who served as Chakotay's right-hand man aboard the raider Val Jean. When he became stranded in the Delta Quadrant aboard the Starfleet vessel USS Voyager, he joined its crew as a security officer.
Ayala was awarded the rank of lieutenant junior grade, initially in the engineering and operations divisions, but eventually in security. He was generally assigned to the bridge as a relief tactical officer. He also served as operations officer at various points in 2371 and 2372. Ayala was left in command of the bridge when the ship was affected by a distortion ring being.
In 2375, while Lieutenant Commander Tuvok was missing with an away team aboard the Delta Flyer, Lieutenant Ayala served as acting tactical officer. With the crew at continuous work to find the away team, Captain Janeway asked him to contact the Beta team on the surface, as they had not reported in for an hour. At the same time, Neelix also offered the bridge crew some coffee, of which Ayala accepted a cup.
By 2378, shortly before Voyager returned to Earth, Ayala had switched to the command division, and was assigned to the conn.