The club reached the First Division in his time there, and he also played in their 2–1 victory over Premier League side Leeds United in the third round of the FA Cup in January 2002.
[4] In 2004, Bonner joined Oldham Athletic but suffered a career ending injury in September 2005 after breaking his arm in a match against Port Vale.
[7] After seven years and four managers in his time at Bloomfield Road, Bonner moved south to join Cardiff City in 1998 on a free transfer after turning down a new contract at Blackpool, stating "I felt I was going a bit stale and I needed a new challenge.
[5] After recovering from the injury, he managed to force his way back into the side that had seen an injection of funds from chairman Sam Hammam that saw a number of new signings arrive, including Graham Kavanagh, Spencer Prior and Neil Alexander.
Bonner played a key role in the club's promotion to Division Two, forming a central midfield partnership with Willie Boland,[6] stating that the pair did the "donkey work" to allow the rest of the team to focus on attacking.
[13] He also played in the 2003 Football League Second Division play-off final at the Millennium Stadium as a late substitute in place of Andy Legg as Cardiff defeated Queens Park Rangers 1–0 to win promotion.
[7][14] He was also part of the side that caused a FA Cup upset by defeating Premier League leaders Leeds United in the third round during the 2001–02 season.
He grew unhappy after he and teammate Gareth Whalley were excluded from the side due to a potential contractual bonus being triggered if either of the pair played another league fixture for the club.
"[18] Bonner joined Division Two side Oldham Athletic in March 2004 on a deal until the end of the 2003–04 season, becoming Brian Talbot's first signing since being appointed manager.
[17] After criticising Cardiff for not triggering the £50,000 bonus payment for matches played, he was rebuffed by Lawrence who commented "I have never heard such nonsense in my life.
[24] 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.