On 28 September 2005, having just signed a new contract extension at the club, Bonner played in a 2–2 draw with Port Vale but suffered a severely broken arm in the opening five minutes of the match after colliding with a Port Vale player. He was quickly replaced by Richard Butcher, before being transported to a local hospital for treatment. His arm was pinned back together and he was originally expected to be out for eight weeks. However, his arm failed to knit back together correctly and, in November, this was eventually extended to an estimated three months out. He was forced to undergo a second operation where surgeons were able to graft bone from his hip onto his arm, which was eventually secured using a metal plate and nine pins. He was forced to retire from football at the age of 32 on medical advice after being warned of potential permanent disability if he injured the arm again.