On May 15, 1999, the USHL unanimously voted to allow then Omaha Lancers' owner, Ted Baer, to place a new team in Kearney, Nebraska, for the 2000–01 season.

In the following 2002–03 season, during the midst of a 10-game losing streak in mid-December, Jim Hillman resigned as coach and general manager.

The team featured future National Hockey League players Bill Thomas, Mark Van Guilder, and Peter Mannino.

It qualified for the playoffs for the fourth consecutive season, narrowly beating out Sioux City for the final spot in the division.

Under Hauge, the Storm rallied late in the season and was able to clinch a playoff spot, finishing in sixth in the Western Conference.

Head coach and general manager Jim Hulton was relieved of his duties in the 2015 off-season and replaced by Bill Muckalt.

Goaltender Jake Kielly set the Storm's single-season record for best save percentage (.919) and went on a 19-game point streak during the middle of the season.

Wade Allison was named Clark Cup most valuable player and the Philadelphia Flyers selected him in the second round of the 2016 NHL Entry Draft.

Goaltender Jake Kielly set the Tier I USHL postseason record with a .950 save percentage and also had a 1.64 goals against average.

On February 6, the Storm moved assistant captain Joey Matthews, second-leading scorer Charlie Kelleher, and Odeen Tufto to Sioux City for draft picks and a player to be named later.

The same day, Tri-City executed two separate trades with Waterloo, moving captain Alex Limoges (for forward Caleb Rule, a draft pick and a player to be named later) and starting goaltender Dayton Rasmussen (for D Tyler Borsch).

Tri-City sent a league-high five players to the 2017 USHL/NHL Top Prospects Game and forward Paul Washe was named Team West MVP (two goals) in Sioux Falls.

Prior to the 2017–18 season, Muckalt left the Storm to become the associate head coach at his alma mater, the University of Michigan.

Former Youngstown Phantoms and Orlando Solar Bears head coach, Anthony Noreen, was named as his replacement.

[1] Noreen led the team to an Anderson Cup regular season championship in 2018–19 and won USHL Coach of the Year.

[2] Notable former players who have continued to play professionally include Mason Appleton, Blake Coleman, Christian Hanson, Jack Hillen, Nick Lappin, Jarod Palmer, Scott Parse, Jaden Schwartz, Bill Thomas, and Mike Vecchione.