They went on to repeat as champions, defeating the Phoenix Mercury in the first-ever WNBA Finals, which had become a three-game championship series.

In 1999, led by what was already known as the Big Three, (Cynthia Cooper, Sheryl Swoopes and Tina Thompson), the Comets survived a stunning last-second, half-court, buzzer beater by the Liberty's Teresa Weatherspoon in Game 2 -- as it appeared the Comets were set to win the title -- to beat the Liberty in three games and win their third straight title, this one after the death of teammate Kim Perrot, who died of cancer.

Despite playing without the two biggest stars from their title runs, Houston made the playoffs with a 19–13 record before falling in the first round to the eventual champion Los Angeles Sparks.

In October 2006, team owner Leslie Alexander – who also owned the Houston Rockets -- announced he was selling the Comets, and longtime head coach Van Chancellor resigned in January 2007.

On January 31, 2007, the WNBA Board of Governors approved the sale of the team to Hilton Koch, a Houston-based mattress and furniture businessman.

On December 12, 2007, team owner Hilton Koch announced that the Comets would be moving from the Toyota Center to Reliant Arena for the 2008 WNBA season.

[7] The Comets played their final home game on September 15, 2008 at the Strahan Coliseum on the campus of Texas State due to Hurricane Ike.

[7] In April 2024, the Rockets, now led by Tilman Fertitta, had submitted to the WNBA to revive the Comets franchise and intends to retain the team's branding if successfully landing an expansion bid.