In his estate, Arnold Stromwell, Gotham's reigning crime boss, is watching the evening news. The lead item is the worsening conflict between himself and upcoming boss Rupert Thorne. That much he knows, but he is shocked to hear on the news that his son, Joey, has been missing for days. He and his son were estranged, but Stromwell is convinced that Thorne is behind this. He orders his men to set up a meeting with Thorne.
Batman, disguised as a hobo is eavesdropping on Thorne when he receives Stromwell's message, and plots to assassinate Stromwell. On the way to the meeting, Stromwell passes an old rail yard, and has a flashback: two young boys, Arnie and Michael, are arguing on their way home. Arnie has stolen a handful of candy, and Michael refuses to take any. Arnie swears that one day he will "own" Gotham. But as they walk home, a train roars up the tracks at the boys. Michael dives out of the way, but Arnie's shoe is stuck...
Shaking off the memory, Stromwell enters a deli controlled by Thorne for the meeting.
Elsewhere, Batman approaches an elderly priest and asks for his help.
Thorne acts affable, but Stromwell seizes him and demands to know where his son is. Seeming genuinely surprised, Thorne swears he had nothing to do with Joey's disappearance. Calming down, Stromwell accepts Thorne's invitation to sit - then realizes he has been set up as Thorne and the deli owner run out the back. A bomb inside the deli explodes. Stromwell is knocked unconscious, and trapped by the flames, but Batman enters and pulls him free. When Stromwell regains consciousness, Batman confronts him, asking him to give up his criminal ways and turn state's evidence. Stromwell acts defiant, but Batman decides to take him on a "tour" - first to Arnie's old neighborhood, where he started as an ordinary drug peddler, then to Sunrise Foundation, a drug rehabilitation center. Inside, Stromwell is shocked to find his estranged wife, Connie, who is attending to Joey, suffering from severe drug withdrawal pains. Stromwell rages, but is brought up short when Connie said it was one of his own dealers who got Joey addicted.
Appearing contrite, Stromwell agrees to hand over files incriminating himself and Thorne to Batman. But at the empty office he leads Batman to, Stromwell slips Batman a stack of dummy files, and uses his distraction to grab a gun, saying he won't go down so easily, and once he's finished with Thorne, he'll "rescue" Joey from the rehab center. Then they are both attacked by Thorne and his gang, who overheard a bum that witnessed Stromwell's escape at Batman's hands. Batman subdues Thorne's thugs, while Stromwell flees, with Thorne himself in pursuit. As Stromwell runs, he finds himself back at the old rail yard, and remembers the rest of the flashback: Just before the train hits, Arnie manages to get his shoe free, and stumbles out of the way - straight onto the next track as a second train is bearing down on him. Michael pushes Arnie out of the way, and the train roars over him, Arnie screaming "Michael! Michael...!" Stromwell collapses, sobbing "Michael... Michael..." A voice answers, "I'm here, Arnie." The old priest steps into the light - Father Michael Stromwell. He wasn't killed, but lost a leg - something for which Arnie never forgave himself. Out of guilt, he angrily says he doesn't need Michael's help, to which Michael reminds him of the current dismal state of his life: his family is broken, his son is gravely ill, his empire is crumbling, and his enemies are closing in. Michael appeals to Arnie, asking him to do the right thing: "[F]or yourself, for your son, for me, your little brother." Arnie hugs his brother, sobbing.
Then both of them are menaced by Thorne, with a gun, but Batman arrives just in time to save them. The police arrive on the scene. Thorne is arrested, and Arnie, arm in arm with his brother, prepares to give a statement to the police. Batman, his work done, slips away into the night.