In the 2003–04 season, the Vipers reached the J. Ross Robertson Cup finals, but lost to the Aylmer Blues 4-games-to-2.

After finishing the regular season in second place with 17 wins in 30 games, the Vipers knocked off the Cambridge Hornets 4-games-to-3 to make the league finals.

The team filled the gap when the disgruntled Cambridge Hornets left the MLH, the collegiate Windsor St. Clair Saints, walked away from the league.

The Vipers decided it was their time to leave as well and applied to join the Western Ontario Athletic Association Senior Hockey League.

The Thunder had a successful first season in the WOAA, earning a record of 11-7-2, registering 24 points, and fifth place in the South Division.