Blasting through the Rocky Mountain Football League in it's inaugural season of 1999, the Rebels went undefeated and won the RMFL championship 36-28 over the Treasure Valley Cowboys.  There was a mid-season forfeit awarded to the Blackfoot Dragons, a team Snake River defeated 44-0 in the opener, 28-6 in week four and again 82-6 in the opening round of the playoffs in what is still the most lopsided playoff games in Northwest history.  Quarterback Jeff Dalley was named RMFL MVP and defensive end Rick Anderson won the Defensive MVP award.

Following that title win, Snake River embarked on a two-season odyssey as an independent team in 2000 while being courted by the North American Football League attempting to expand into the western states, and as a member of the Utah Football League in 2001 where they were defeated by the South Ogden Rhino-Raiders in the UFL championship game.

Returning to the RMFL for 2002 and out to a 6-1 start, an issue arose over league fees and the RMFL suspended the Rebels and disqualified Snake River from playoff contention.  Jeb Harrison placed his name in the final game against Helena with five sacks in the 54-19 win.

Back in good standing for the 2003 season, the Rebels were tripped up early to start 2-2 before winnning five straight to reach another RMFL championship game.  The Idaho Mustangs awaited and exacted revenge for a week six loss, taking the RMFL crown 21-8 where the Mustangs forced six Rebel turnovers snapping a 7-0 win streak Snake River owned over Idaho Falls.  Six players made All-RMFL 1st or 2nd teams, and cornerback Dustin Aldous earned American Football Assocation third team all-america honors.

Prior to the start of the 2004 season, management made the decision to shut down operations after posting a 41-9 record over five seasons and most of the players joined forces with former Pocatello Silverbacks to form the Pocatello Predators.

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