Under owner/head coach Bill Arbogast Blizzard's first season in competition began strongly with back-to-back wins in their first two games, 4–0 over Kansas City Brass and 4–3 over state rivals Boulder Rapids Reserve, with Sean McGinnis and Daniel Wasson finding the net.

Blizzard finished their first campaign 7th in the Heartland Division, 35 points adrift of divisional champions Chicago Fire Premier.

However, this victory did not signal a turnaround in fortunes: they lost five of their next six games, beating expansion side Springfield Storm 3–1, but suffering heavy defeats to El Paso Patriots (3–0), Boulder Rapids Reserve (5–1) and BYU Cougars (6–2).

This was as good as it got for Blizzard: most of the rest of the season was spent enduring a series of heavy defeats, including a 4–1 thrashing at home by Des Moines Menace, a 6–1 demolition at the hands of Colorado Rapids U23's, a 3–1 loss on the road in Sioux Falls, and a 1–0 loss to Kansas City Brass on the final day of the season in what turned out to be the franchise's last ever game.

Blizzard finished 2006 6th in the Heartland Division for the second consecutive year, three points ahead of Thunder Bay Chill, but 30 behind divisional champions Colorado.