Bower helped rebuild the Hornets, despite the troubles Hurricane Katrina placed on the club and the city of New Orleans in general. He took a giant step in re-writing Hornets history by trading franchise piece Baron Davis to the Warriors, then selecting guard Chris Paul fourth overall in the 2005 NBA draft. The disaster Katrina caused forced the Hornets to move to Oklahoma City until the 2007–08 NBA season, but Bower continued to build his club. Through trade, draft, and signings, the Hornets actually competed in their two seasons in Oklahoma with a 38–44 record in 2005–06 and 39–43 in 2006–07. Yet again, another series of trials and tribulations, the Hornets improved and contended. Injuries to Paul, Peja Stojaković, and scoring big man David West dampened the opportunity to make the playoffs. For 2007–08, the Hornets came back home to open arms. They broke out, with the dangerous roster of Tyson Chandler, Paul, Stojakovic, West, and new acquisition Morris Peterson, with pieces like 3-point specialists Rasual Butler and Jannero Pargo and rebounders Melvin Ely and Ryan Bowen; and developing youth such as Julian Wright and Hilton Armstrong. The general of it all was Coach of the YearByron Scott prior to the 2004–05 NBA season, and the Hornets won 56 games, their first divisional title, and were labeled "contender" by many analysts. Bower's performance in spearheading the Hornets from lottery team to contender gave him 12 votes from the sportswriters for the Sporting NewsNBA Executive of the Year, behind Lakers' GM Mitch Kupchak and winner, Boston Celtics' Danny Ainge. Bower helped draft David West, J. R. Smith, Chris Paul, Darren Collison and Marcus Thornton. Bower had been with the organization for 14 years, beginning in 1995–96, director of scouting, director of player personnel, as a scout, GM, and assistant to former coaches Paul Silas and Tim Floyd. Bowers served as an advance scout for the Charlotte Hornets in 1995–97 and the Hornets Director of Scouting in 1997–2009. He also was an associate head coach at Marist College from 1990–95, prior to that, being an assistant coach at both Marist and Penn State University.
Head coach
On November 12, 2009, Bower was made the head coach of the team after the firing of Byron Scott. He led the team to a 34–39 record despite injury problems in the team. At the end of the season, he stepped down from the coaching duty and returned to his position as a general manager. He was replaced by Monty Williams. Bower and the Hornets parted ways on July 13, 2010.
Marist
On April 10, 2013 it was announced that he will take over as coach of the Marist College men's basketball team. Bower served as an assistant coach for the Red Foxes from 1986 to 1990 and served as the Associate Head Coach from 1990 to 1995. He was involved in the team's 1987 NCAA Tournament appearance and ECAC Metro Conference regular-season championships in 1987 and 1988. Bower also aided in the development of Rik Smits, the second overall pick in the 1988 NBA Draft by the Indiana Pacers.
Detroit Pistons
On June 3, 2014, Bower was named the general manager of the Detroit Pistons. On June 13, 2016, the Pistons signed Bower to a contract extension. Under Bower, the Pistons reached the playoffs in his second season as the general manager. However, on June 1, 2018, Bower was fired from his position as general manager of the team.
Phoenix Suns
On April 11, 2019, Bower was named a senior vice president of basketball operations for the Phoenix Suns Under this new title, Bower helps relay certain information towards general manager James Jones when necessary.