Nevertheless, it was a very promising first season; future MLS star Herculez Gomez was the Gauchos' top scorer, with 17 goals, while goalkeeper Daniel Sirota posted an impressive 1.36 GAA average.

They lost 3–0 to Fresno Fuego at home in mid May, were hammered 4–0 by Utah Blitzz, received five of the best from Western Mass Pioneers on the road in June, and received a 5–1 shellacking from an Orange County Blue Star team that boasted Jürgen Klinsmann and future MLS star Robbie Rogers in their starting eleven.

They won their opening game of the season, 2–1 over BYU Cougars, and recorded an astonishing 3–2 victory over Orange County Blue Star in June, coming back from 2 goals down to take the win on a Herculez Gomez hat trick, despite both teams having been reduced to nine men by full-time!

The Gauchos also made their second trip to the US Open Cup this year, but unexpectedly lost to PDL side Boulder Rapids Reserve in the second round 5–4 on penalties after a 0–0 tie in regulation time.

Despite the better on-field performances, during the 2004 off-season the team's management made the decision to self-relegate themselves to the USL Premier Development League for 2005.

Gold were the Gauchos' whipping boys in 06, with the San Diego team winning 2–0 and 6–0 in their other encounters, the latter of which featured a Dustin Guerrero hat trick and a brace from Dagoberto Nogales-Gallegos.