A shadowy figure makes his way through the harbor through the canals then emerges and takes to the rooftops. Elsewhere a gang of three crooks break into a building and the figure spots them and confronts them. He demolishes their getaway car and is revealed as a humanoid alligator. He quickly takes them out and "persuades" them to work for him, announcing his name is Killer Croc.
Bruce is in the Batcave trying to string together the pattern to a recent series of seemingly unrelated crimes. Alfred is busy cleaning up Bruce's collection of evidence and archiving them in a "private museum." Bruce figures out the robberies were all near water and goes to investigate. Croc's new gang are committing another robbery when the Batman intervenes. He takes out the three of them while Croc secretly looks on then confronts the hero, sending compressed canisters of oxygen at him. Then they fight and Croc knocks Batman into the waters where he clearly has the upper hand.
The Batman gets free and rides one of the oxygen tanks back to the surface just as his air runs out, but Croc and his men have escaped. The three gang members use scuba gear to get to Croc's headquarters where Croc reveals how he plans to flood the city. In the Batcave, Alfred isn't happy at Bruce's wet costume and they intercept a newscast of the flood. Then Bruce picks up three bank alarms in the flooded financial district and goes to investigate on his own Bat-ski, wearing a special costume. Croc's men flee in separate directions while Croc engages in a game of "chicken." Batman pursues him through the flooded streets while Croc's men close in. Batman is knocked free in the distraction and takes out one of the men - interrogation reveals the guy has no idea what Croc's background is, but that the flooding is just the first step in Croc's plan.
The guy reveals Croc's location and Batman uses his jet ski and his underwater costume to get there. He finds the stolen loot and Croc's plans. Croc arrives and reveals his plan - reverse the pumps that send excess water into the bay. Croc unleashes his two pet crocodiles and departs. Batman uses explosives to seal them in a tunnel and goes after Croc at the pumps. Batman takes out the two remaining goons and temporarily stuns Croc, then reverses the pumps. Croc comes after Batman and throws him into the waters, then reverses the pumps again.
A stunned Batman emerges from the waters and the two fight - they're evenly matched but Batman is forced to divert his attention by reversing the pumps. Once he succeeds, Croc garbs him and takes him down into the sewer waters - Batman realizes that Croc isn't a waterbreather and breaks free to use his own rebreather, then uses a batline to keep Croc underwater until he runs out of breath. Batman leaves them all for the police - he has a new relic for the exhibit hall, one of Croc's teeth.