Upon joining the AHL for the 2001–02 season, they became the primary affiliate of the one-year-old NHL expansion team, the Minnesota Wild, a partnership they maintained until the franchise's relocation in 2013.

As of November 2023, Cal Clutterbuck, Jared Spurgeon, Matt Dumba, Charlie Coyle, Darcy Kuemper, Jonas Brodin and Jason Zucker are the only players active in the NHL who had once spent time in Houston.

The Aeros posted a winning record in their inaugural season and made the playoffs, while the team repeatedly sold out its home games at The Summit after not having professional hockey in the region for nearly two decades.

Some of these signings included Mark Freer, who set the Houston franchise record for career goals, eventual coach Mike Yeo, veteran NHL player Jim Paek, and goaltending duo Frederic Chabot and Manny Fernandez.

Houston won 44 games in 1996–97 and followed that with their first 50-win campaign the next year, losing in the 1998 Western Conference Finals to the Long Beach Ice Dogs.

[1] By the start of the 1998–99 season, the Aeros were led by the goalie tandem of Chabot and Fernandez posted a combined 2.35 goals against average, the best average in the league, minor league journeyman Jeff Christian scored a team-leading 45 goals and 109 points (including 88 assists) from former Michigan Wolverines' player Brian Wiseman.

As a result, the NHL actively encouraged its owners to reassign their development operations to clubs in the American Hockey League (AHL), the chief rival of the IHL.

Due to Houston's George Bush Intercontinental Airport making travel for prospects easier, the Wild entered an agreement with the Aeros as their top development affiliate.

Todd McLellan was installed as head coach by the Wild and the Aeros made the Western Conference Finals in their first AHL season before falling to their old IHL rivals, the Chicago Wolves.

As NHL teams began to build stronger ties with their farm clubs, the Aeros colors were changed to match the Wild's forest green and iron range red with wheat accents.

Since the 1990s, Watson operated The Summit, which acted as the home arena for both teams, and had control over the lease agreement with the Rockets, which had been purchased by Alexander in 1993.

[citation needed] The AHL and NHL both entered the negotiations and the Aeros and Rockets agreed to a new seven-year agreement that ran through the 2012–13 season.