On 8 November 2008, during a 2–1 defeat at former club Barnsley, Morgan elbowed Iain Hume as he was waiting for an aerial ball, and Hume suffered a fractured skull as a result whilst Morgan received only a yellow card. Hume underwent emergency surgery and spent 48 hours in the high-dependency unit of a Manchester hospital with life-threatening injuries. The Football Association chose not to charge Morgan as referee Andy D'Urso had shown Morgan a yellow card at the time of the incident; this was despite Barnsley Central MP Eric Illsley calling an Early day motion in Parliament for the FA to review their decision. Barnsley and Hume considered taking legal action against Morgan, who described the period since the incident as "a test of character". Morgan went on to make a total of 50 appearances throughout the 2008–09 campaign, helping the club to qualify for the play-offs with a third-place finish, however they lost 1–0 to Burnley in the play-off final at Wembley.