Killer Croc is having a nightmare wherein he sees himself being tortured by the orderlies at Arkham Asylum. Lashing out, he attacks one of his new friends in his underground shelter. An elderly woman named Aunt Marcy consoles Croc and convinces him to release the frightened homeless man. Croc calms down and sets to improving the living conditions for his new acquaintances. Aunt Marcy's son asks Croc about his missing dog Spot. Croc tells him that he will look for the animal for him.

Meanwhile, Batman investigates a break-in at Taylor's Exclusive Shopping outlet. He finds a hidden stairwell behind one of the snack machines and descends it. Batman radios Robin at the Batcave who provides him with schematics of the entire Gotham City underground maintenance system. Batman tells him that he suspects that Killer Croc may be responsible for the robbery, and Robin warns him to stay clear of the water tunnels. The city is implementing a new delivery system, and the tunnels are scheduled to be flooded at midnight.

Batman takes Ace with him and together they begin exploring the labyrinthine tunnels. Ace runs into a sewer pipe and finds a lost dog named Spot. He saves Spot from a pack of hungry rats. Batman catches up with Ace and soon discovers a weakened section of wall. He breaks it down and finds that it leads to the fallout shelter where Killer Croc's friends reside. Croc catches Batman's scent and attacks him. The two begin fighting and Batman barely manages to evade Croc's crushing blows. Suddenly, he hears the sound of rushing water. Batman shouts to Croc, warning him that the tunnels are going to be flooded. Croc presses up against the weakened wall, enabling Batman the chance to get Aunt Marcy and the others to higher ground. The water bursts through the crumbling mortar and Croc is washed away. Aunt Marcy and the others believe that he dies in the flood.

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