Peter Pauling was a corrupt GCPD Commissioner that answered to Rupert Thorne.
James Gordon(forced out of office) and private Detective Jason Bard began a private investigation of Pauling's corruption.Pauling hired corrupt cops to assault Gordon. Gordon had to be hospitalized, but he only took it as proof that he had Pauling on the run. And Batman and his associates took turns guarding Gordon's hospital room to make certain he was safe.
Boss Rupert Thorne's mental state became more and more precarious, as Professor Hugo Strange was tormenting him with "special effects" .Thorne though he had murdered Strange, but the Professor had survived. Thorne eventually though Mayor Hamilton Hill was trying to cut him out of their partnership, and he barged into Hill's office wildly firing a gun.Pauling was killed in the crossfire,and Thorne was judged insane and not prosecuted.