Complex sentence: McGowan was initially a first-team player but an injury during 1999--2000 limited his appearances, and he left the club on a free transfer in 2001 after a clearout by new manager Joe Kinnear.
Split into simpler sentences: McGowan was initially a first-team player but an injury during the 1999--2000 season limited his appearances. Unable to play to the best of his ability, he left the club on a free transfer in 2001 after a clearout by recently employed manager Joe Kinnear.