Bootsma played the first 10 games of 2001 and had more than 20 possessions in 5 of them. However, the tumultuous round 10 match against Richmond, Ben Allan's first as caretaker coach after Damian Drum was sacked, would be Bootsma's last, due initially to a knee injury and later he was unable to break into the team eager to rebuild for the future. He would remain on the Fremantle list for the 2002 season, but did not play another senior game. He retired from AFL football at the end of 2002.