After that, however, City would only win three more league matches before Christmas, as the heavily overhauled squad struggled to come together, with injuries only compounding the situation.
The club would hit its lowest ebb after an embarrassing 2–1 loss to York City in their final pre-Christmas fixture, a result which left them 12th in the table and led to fans calling for Royle's sacking.
City's poor first half of the season, combined with the form of runaway leaders Fulham and second-placed Walsall meant that an automatic promotion challenge was never seriously on the cards, but they secured third place on the final day of the season, and also exacted revenge on York City for their earlier humiliation by thrashing the Minstermen 4–0, condemning them to relegation.
The play-off final was goalless for 82 minutes, before the Gills struck a pair of late goals that looked to have ensured that City would be spending a second successive season in Division Two.
In the FA Cup, City beat Halifax Town first, then Darlington in a replay with an extra time winner, before losing to Wimbledon by a single goal.