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, stating that the pair did the "donkey work" to allow the rest of the team to focus on attacking. Having come close to leaving the side in March 2003 after falling out of favour under manager Lennie Lawrence, Bonner commented "I got my head down, trained hard and have forced myself back into the side". He also revealed that he had considered handing in a transfer request to Lawrence several weeks prior.