Bones was signed by the Padres as an amateur free agent on May 13, 1986, making his MLB debut on August 11, 1991, against the Cincinnati Reds.

On March 26, 1992, Bones was traded with Matt Mieske and José Valentín to the Milwaukee Brewers for Gary Sheffield and minor league player Geoff Kellogg.

On August 29, 1996, the Brewers traded Bones, Pat Listach, and Graeme Lloyd to the New York Yankees for Bob Wickman and Gerald Williams.

[8] In June 2000, a Florida Marlins clubhouse attendant found a paper bag in Bones' locker containing over two dozen syringes and six vials of anabolic steroids.

Bones later admitted in an interview with Mitchell Report investigators that he was self-administering steroids and painkillers at the time pursuant to a prescription he was given in his hometown in Puerto Rico.