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 two 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, and 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, Batman watches the news of Bullock, cleared of all charges, warning criminals to beware because he's "back and ready to kick butt!"
Tropes in this episode include:
- Absurdly Spacious Sewer: Killer Croc managed to escape and hide in the sewers beneath Gotham, because apparently the police never check there.
- Adaptational Name Change: Rather than Waylon Jones, Killer Croc's real name in this continuity is revealed by Summer Gleason at the end as "Morgan, first name unknown."
- Badass Boast: From Bullock, after everything is said and done: "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!"
- Best Served Cold: Croc's entire motive is revenge on Bullock for busting him, although he also has animosity towards Conway and Joey for testifying against him in the same case.
- Eureka Moment: Batman realizes the nature of his foe due to Alfred's offhand comment that he was going to keep dinner in a crock pot to keep it warm.Batman: Alfred! You're beautiful! [dashes off]
Alfred: Imagine if I'd gotten around to telling him about the salad.
- Genius Bruiser: Killer Croc makes his debut with a pretty clever plan to frame Bullock.
- Not Me This Time: Rupert Thorne was one of Batman's first guesses, because "Spider" Conway, the first kidnapped victim, was going to testify against Thorne.
- Oh, Crap!: Bullock's expression when the cops came to arrest him after being framed by Killer Croc.
- Plea Bargain: The episode starts with "Spider" Conway offered a reduced sentence in exchange for testimony, and he's frightened that Thorne might get to him first. Unfortunately, Thorne isn't the biggest threat to him.
- Professional Killer: Batman learns from his research that Killer Croc became a hired killer when he came to Gotham City. Bullock arrested him for a union-related murder, which Croc has neither forgotten nor forgiven.
- Roaring Rampage of Revenge: This is the basis for Killer Croc's entire plot. He has a grudge against Bullock for arresting him for murder, and against Conway and Martin for testifying against him in exchange for plea deals. Now it's payback time, as Batman aptly puts it.
- Somewhere, a Herpetologist Is Crying: No, crocodiles do not make their lairs in underwater caves. Crocodiles don't make "lairs" at all, just wallows or nests. And they make those in the open where sunlight can warm them.