BATMAN #415 (1988)
Spoiler Alert: This book takes place after the Millennium #2.
To his utter amazement, Batman has just been pistol-whipped and pushed out a window by a man he believed to be his staunch ally, Commissioner Gordon. Saving himself by grabbing a building ledge, Batman dodges Gordon's bullets and swings back inside the GCPD Headquarters to confront the being he now realizes is actually a Manhunter, but the impostor has already escaped. After listening to a passing conversation, Batman deduces that the Floronic Man, currently a prisoner at Arkham Asylum for the Criminally Insane, is one of those "chosen" by the Oans for their Millennium Project and thus a target for the Manhunters, and he returns to the Batcave.
Meanwhile, in Tannersville, a rural community outside Gotham City, Robin has trailed the Scarecrow to his hideout in an abandoned barn. Impulsively shattering the villain's vials of fear gas, he causes the Scarecrow's own weapon to render him helpless, and apprehends the costumed criminal. Robin takes a comatose Scarecrow to the Batcave, as he was told to just follow the villain and not to take action. Robin's failure to follow orders is punished by Batman, but he realizes Robin has given him a perfect chance to meet with the Floronic Man.
That night, Batman and Robin infiltrate Arkham Asylum under the very noses of the fake Commissioner Gordon and his men, arriving in an ambulance disguised as a badly-beaten Scarecrow and his attending physician. They use the Scarecrow's fear gas to overcome a score of the asylum's most dangerous inmates, whom "Gordon" has released in the exercise yard under guard, then use drug-tipped darts to put most of the police officers and guards present out of action. In a skirmish with the two crimefighters, the ersatz Commissioner is finally revealed as a robot when he is accidentally hit by a shotgun blast by one of "his" own men. Finally, Batman is forced to destroy the robot with a plastique explosive and, having to choose between interrogating the Floronic Man to stop the Manhunters and seeking out the real Commissioner Gordon, he and Robin depart, choosing the latter.
Back at the Batcave, data contained in the severed head of the Gordon robot reveals that the true Gordon has gone to Louisiana and Batman heads down towards that place.