Micheal Atkins was trusted GCPD member who was appointed by James Gordon to be the Chief of Police after the city's period as a 'No Man's Land.
When Gordon was shot by Officer Jordan Rich and retired, Atkins became the new commissioner. Some felt Atkins felt that Atkins would be a good leader and other's felt he cared about playing politics with City Hall instead of catching criminals which was indeed true.
Atkins always had a bad relationship with Batman like rejecting Batman's request for control over the entire police department when various gangs of Gotham City engaged in a devastating gang war. Batman recruited all the police officers which stopped the gang war which angered Atkins and made all costumed vigilantes illegal. Atkins was jealous of Batman's success.
At some point during the 'missing year', Atkins was removed from office since he was implicated for corruption in the force during the time when Batman, Superman, and Wonder Woman all retired from public duty.