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In Darkness Dwells is the fourth story from Batman: Gotham Knight.

The police respond to a riot in a cathedral where Cardinal O'Fallon was giving a sermon. According to eyewitness testimony, the Cardinal was abducted by a large lizard-monster and taken down into the crypts below the cathedral. Lieutenant Gordon, Crispus Allen, and Anna Ramirez investigate; Gordon has a brief conversation with Batman, who agrees with Gordon's theory that the Scarecrow's fear toxin is behind the riot as the doctor has been at large since the riot at the Narrows (during the event of Batman Begins). Batman gives Gordon an earpiece that will allow them to stay in contact and descends below ground, trying to find Cardinal O'Fallon and his abductor. A homeless man living in an abandoned subway station identifies the abductor as Killer Croc. Batman and Gordon briefly discuss the villain's past, but are cut off when Killer Croc himself shows up, under the influence of the fear toxin, and attacks Batman. Batman defeats him, but not before sustaining a bite that transfers some of the toxin to him. He then finds Cardinal O'Fallon being put on trial and sentenced to death by the Scarecrow, who is unhappy with O'Fallon's efforts to help the homeless. Batman leaps in to defend the Cardinal. Using the methane already present in the room, he sparks an explosion that destroys several water pipes, flooding the area and allowing him to escape with the Cardinal. Gordon appears in a helicopter to retrieve the Cardinal and offers to help Batman as well, but Batman refuses, saying, "Maybe next time."

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