The following seasons, the Vipers began to sink to the bottom of the standings and were fortunate to qualify for the playoffs, only to exit the first round.

Vaughan's best season came in 2007–08, when the team boosted a 41–4–4 record, despite finishing 2nd place in the OPJHL's South Conference behind the dominant St. Michael's Buzzers.

In their final 2011–12 season, the Vipers finished 2nd behind the St. Michael's Buzzers, but would lose a heart-breaking series to the Toronto Lakeshore Patriots in 7 games.

Marcus Hinds scored the final goal in Vaughan Vipers history just over 11 minutes into the third period in a 4–2 loss to Toronto at the Al Palladini Community Centre in front of 323 fans.

The news came as a shock, as the Vipers were potential top team in the OJHL and surprise to head coach/general manager Jason Fortier, who had just came up with some marketing ideas for the team, but owner Al Doria claimed it was too late and went ahead with the buyout option offered by the league.