On a rainy night, a police ship is escorting “Spider” Conway, a convict turned witness, who is terrified for some reason. Commissioner Gordon is confused, seeing how Conway will get a 10-year parole in exchange for testifying against Rupert Thorne, but Harvey Bullock notes that Conway fears someone else getting to him first. Suddenly, a strange man places a bomb on the boat and kidnaps Conway. The officers make it to the docks as the boat explodes, and Bullock, dropping his toothpick, has his men search the area. Batman does his own investigation near Stonegate Prison and finds a toothpick on the docks.
Back at GCPD, Bullock is shocked that Gordon is taking him off the case. Gordon explains that since Thorne is a prime suspect, "ugly ancient history is bound to come up". Batman, listening in, decides to investigate Harvey. He takes Bullock’s police file, which Bullock notices is missing shortly after.
At Wayne Manor, Alfred reads the file and learns Bullock was suspected of taking bribes from Thorne 2 years ago. Spider Conway was working for Thorne at the time and had implicated Bullock. The case was dropped for lack of evidence, but Bruce suspects Bullock may have been behind Conway’s kidnapping.
Meanwhile, Conway wakes up in an underwater cavern. Suddenly, a mysterious figure rises out of the water and corners the terrified man.
Batman interrogates Thorne, but Thorne admits that Conway lacks substantial evidence against him, so he does not care about Conway. Batman is now almost certain Bullock was behind the bomb, but Gordon refuses to believe this, insisting that Bullock is clean.
Someone dressed as Bullock busts Joey “the Snail” Martin out of custody and Bullock is arrested. Batman however analyzes a scale he found on the docks; it has a human cellular structure but a reptilian appearance. Batman realizes Bullock may actually be innocent and gets an idea when Alfred mentions a “microwavable crock”. After examining a crocodile exhibit at Ocean World, Batman takes the Batboat to an underwater cave, where he finds the kidnapped criminals. As he unties them, Killer Croc, a criminal with a crocodile like appearance, attacks. Killer Croc easily overpowers Batman in strength, but Batman manages to tie him up and catch the fleeing criminals. Croc escapes however.
Back at the Batcave, Batman researches Killer Croc: he used to be a freak show attraction, then a wrestler, an then turned to crime in Gotham city. Bullock arrested him and Conway and Joey testified against him. Now Croc wants revenge.
With the criminals returned, Bullock is released but Croc attacks him in his car. Batman saves Bullock and chases Croc into the sewers. A fight ensues, and though Croc is stronger, Batman manages to defeat him and take him to Bullock.
The next day, Bullock, cleared of all charges, warns criminals to beware because he's "back and ready to kick butt!"
* BadassBoast: From Bullock, "I just want all the scum buckets and dirt bags in this town to know they better lay low, ‘cause Bullock’s back and ready to kick butt!"
* GeniusBruiser: Killer Croc makes his debut with a pretty clever plan to frame Bullock.
* NotMeThisTime: Rupert Thorne was one of Batman's first guesses, because "Spider" Conway, the first kidnapped victim, was going to testify against Thorne.
--> '''Killer Croc''': You know, they used to call Killer Croc the meanest dude in the wrestling federation. Now, they'll call him the guy who iced the Batman.