They lost only nine games as they won the title, but got off to a slow start this term.
The Priestfield outfit failed to win any of their opening 10 games in all competitions before securing back-to-back victories over
which lifted them out of the relegation zone.
By BBC Radio Kent's Gillingham commentator Matt Cole
Results have been poor this season but the timing of Martin Allen's departure still comes as a surprise.
Many fans were calling for his head when the Gills went 10 games without a win at the beginning of the season, but there were signs of a turnaround.
Even after the defeat at Shrewsbury, few thought it would be Allen's final game in charge.
The man they call 'Mad Dog' came with a reputation for volatility and, with a chairman who is famously forthright with his views, there were those who thought it would always be a case of when rather than if the pair fell out of humour with each other.
Paul Scally has expressed his sadness that results have forced him into the decision to sack the manager he appointed last summer.
It'll be interesting to see how much patience the supporters will have with the chairman and the next boss, after the sacking of a manager who many saw as a cult hero, and brought them their first league title in nearly 50 years.
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