The toxin is released and affects everyone in the Narrows including the escaped convicts and the police alike. Gordon inoculates himself with the antidote and finds a fearful Flass ready to shoot two innocent and equally frightened teenagers. Gordon knocks him out and handcuffs him to a railing. Meanwhile the few remaining people of the Gotham Police force wonder what is going on.
The Narrows begins to tear itself apart. In the streets, people violently attack one another. Rachel is confronted by Crane on a horse whose previous rider, a riot cop, is dragged behind. Wearing his burlap mask, Crane announces to her his new alias, 'the Scarecrow.' Gordon requests reinforcements but to his dismay he is told that all of the riot police are already on the island and there is no one left to send.
Suddenly the Tumbler shoots across the gap from Gotham to the Narrows. Batman explains to Gordon that Ra's intends to use the train to carry the microwave emitter to Wayne Tower. When the train reaches Wayne Tower at the center of Gotham, the microwave emitter will vaporise the contents of all the water mains, covering the whole city with the toxin. He asks Gordon for help and gives him the key to the Tumbler.
The Scarecrow is about to run down Rachel. She fires her taser and hits him in the face. His horse carries him away screaming. Rachel is surrounded by a dozen inmates from Arkham, including the serial killer Mr. Zasz, carrying a knife. Batman jumps from above them, cracking Zasz over the head, picks up Rachel and carries her to a rooftop and to safety. As Batman leaves her she asks him who he is.
He replies 'It's not who I am underneath, but what I do that defines me' -- quoting her own words back at her. She says 'Bruce?' as he jumps from the rooftop and uses his memory cloth cape as a glider. As he seemingly flies in the air, the fearful people below shriek in terror as their hallucinations warp the sight of him. Gordon orders the main bridge to be lowered and starts up the Tumbler.
Ra's is overseeing the madness below as his men fasten the microwave emitter into place on board the train. He spots Batman gliding towards him. Batman lands on the train platform. Ra's comments that he took his advice on theatricality a bit too literally and boards the train. Four members of the League appear and prevent Batman from pursuing.
During the fight, Batman tries to uses his grapple hook to secure himself to the train but it is knocked out of his hand. The fight takes all participants down to the street floor where Batman manages to overcome all four League members. However he is ganged up on by dozens of terrified and angry citizens. As Ra's starts the train overhead, Batman finds his grapple gun and fires it at the train. He's dragged behind the train.
Gordon meanwhile is following the Tumbler's GPS system toward Wayne Tower. As the bridges are lowered, Ra's's train breaks the water pipes, releasing the toxic gas. The Tumbler is not far behind. Batman manages to pull himself to the train. He smashes through one of the train windows and engages an infuriated Ra's. Batman takes Ra's sword and breaks it in two with his gauntlets. Distracting Ra's, he stabs the sword into the braking controls of the train.
Gordon arrives at Wayne Tower. He arms the Tumbler's defense systems and fires missiles at a train rail foundation. With the train approaching Wayne Tower, Ra's gets the upper hand over Batman and taunts him: 'Don't be afraid, Bruce. You are just an ordinary man in a cape. That's why you couldn't fight injustice, that's why you can't stop this train.'
Batman replies, 'who said anything about stopping it?' Ra's looks up and notices a half of his sword sticking in the brake control. As this happens Gordon destroys the foundation and breaks the railway line. With this distraction, Batman regains the upper hand and pins Ra's. Batman explains that he won't kill Ra's -- but he doesn't have to save him, either. He blows out the back end of the train car, throws himself out, and glides away.
Ra's can only look up to watch the train propel itself off the line and into the street below. The microwave emitter gets damaged by the impact and explodes, destroying the whole train. The next day, Earle arrives at Wayne Enterprises to chair a meeting. He'd shocked to find that the meeting has already begun -- and is led by Fox, who reveals he has Earle's job.
Bruce is in the back of his car reading a newspaper: Batman has made the front page and Bruce is on page 8 under the headline 'Drunken Billionaire Burns Down Home.' He takes a call from Earle, who asks on what authority Bruce can decide who runs Wayne Enterprises. Bruce states that he is the owner.
Earle reminds him that the company has gone public. Bruce explains that he bought most of the shares through various trusts and brokerages. Fox agrees with Bruce's words, and asks Earle, "Didn't you get the memo?" in reference to the words Earle told him when firing him from AS.
Back at Wayne Manor, Bruce is nailing boards over the old well in the garden when he is approached by Rachel. He apologizes for not telling her about his identity earlier. She apologizes for slapping him the day Chill died and for the horrible things that she said before he disappeared. Bruce tells her that what she said was true and that he was just a coward with a gun. He thanks her. She says that when she heard that he was back she began to hope.
She moves closer towards him and kisses him. She then explains that she then found out about his mask -- his actual face. She explains that his true face is the cowl of Batman and that the boy she loved long ago never came back. But maybe one day they can be together when Batman is no longer needed. Bruce nods. Rachel tells him that she was wrong and that Bruce's father would be proud of him, just as she is.
Alfred is walking through the rubble of the Manor and Rachel asks Bruce about what he will do. Bruce replies that he'll rebuild it just the way it was before. Rachel turns to leave. Alfred wonders if it's a good time to improve the foundations of the south-east corner. Bruce agrees and they walk off.
That night, Batman meets Gordon, who reveals that he has recently been made a lieutenant. Gordon has also made a version of the signal that Batman had made with Falcone. Gordon talks about the escalation between law enforcement methods and criminal methods such as the police wearing Kevlar leading to criminals buying armor-piercing ammunition. He expresses concern that the city's dependence on Batman may have negative consequences.
Gordon uses a recent case as an example. A criminal with a taste for theatrics has killed two people. The suspect leaves a calling card at the scene of each crime. Gordon gives Batman the evidence: a Joker playing card. Batman says that he will look into it. Batman then assures Gordon that they can make Gotham safe again and he jumps from the roof and glides away.