Des Moines began 2006 looking to defend their PDL title, and began the season in the best possible way, rattling off six wins in their first seven games, including a trio of impressive home wins, 3–0 over Colorado Springs Blizzard, 5–1 over Sioux Falls Spitfire and 4–1 over Thunder Bay Chill, the latter of which featured a brace from Armin Mujdzic. Menace enjoyed their fourth US Open Cup campaign off the back of their early form, and for the second year in a row they proved to be formidable opponents for higher league opposition. They beat the Milwaukee-based USASA team Croatian Eagles 4–1 in the qualifying round, and a second amateur team – Dallas Mustang Legends – in the first round proper, before causing a huge upset by knocking out USL First Division powerhouse Minnesota Thunder in the second round 1–0, with the winning goal being scored by Boltnar. In the third round, Menace faced off against the Wizards in the third round second consecutive season; this year, they would hang in the match until Scott Sealy won it in stoppage time. The mid-season saw a slight stutter from Des Moines as they lost three of their next four games, including a pair of demoralizing losses to Boulder Rapids Reserve which would eventually decide the divisional title. Menace did bounce back down the home stretch, remaining unbeaten in their final five regular season games, but the results included two ties against the St. Louis Lions, which left the Rapids ten points clear of Menace at the top of the Heartland Division standings. Menace faced Great Lakes division champions Chicago Fire Premier in the Central Conference Semifinal; the game was an epic one, with Menace hanging on for a 1–1 tie at the end of regular time despite being a man short following a red card. Extra time saw the Menace fight back from two goals down to force penalty kicks after a 3–3 tie; however, the Menace lost the penalty shootout 5–3, ending their title defense. Once more, Boltnar and Disang led the scoring tables with 7 goals each.