Prior to the 2000 season he was elevated to the senior list and played 19 games for the year, including two finals.
He won a Rising Star nomination, averaged 16 disposals a game over the course of the season as well as taking 120 marks, and was heralded as the club's most courageous player.
As Bowyer recovered from his injuries during 2002, he struggled to cope personally with the isolation of no longer being heavily involved in the game or the club.
[3] Late in the year and at the height of his depression, Bowyer traveled to the Greek islands on his own, where he almost lost his life after his left arm was badly cut by glass; the exact nature of this incident has not been publicly discussed.
His efforts for Carlton's VFL-affiliate, the Northern Bullants, in 2005 were good enough to win him the Laurie Hill Trophy as club best and fairest.