Plot

The killer known as Holiday continues to stalk the Falcone crime family while a new class of costumed criminal rises in Gotham City. Batman suspects that a former ally might be the serial killer.

The reign of terror wrought by the Holiday killer continues in Gotham City. With each calculated crime, the stakes rise as tensions boil over between the Falcone and Maroni crime families. As Batman, James Gordon and Harvey Dent race to solve the deadly puzzle, a breach at Arkham Asylum brings villainous players into the game. Based on the critically acclaimed graphic novel, Batman: The Long Halloween - Part Two concludes this gripping chapter in the Dark Knight's saga.

Poison Ivy has been controlling Bruce Wayne for three months and has been forcing him to sign over assets to Carmine Falcone, while unintentionally preventing him from acting as Batman. Catwoman rescues Bruce (and Alfred) from Poison Ivy. In the meantime, the Holiday killings have continued through Valentine's Day, Saint Patrick's Day, and April Fools' Day.

On Mother's Day, Holiday kills the gunmaker that had been supplying his weapons. That night, Scarecrow escapes from Arkham Asylum and ends up in a fight with Batman, and escapes by injecting fear toxin into Batman's abdomen. In a fear-induced hallucination, Batman staggers around Gotham, ending up in Crime Alley, where Catwoman finds him and takes him home. Carmine's daughter, Sofia Falcone, meets with her father after arranging Scarecrow's escape and asks for a seat at his table, which he declines. Dent and Gordon visit Bruce Wayne to get his testimony regarding the night Alberto was killed, with Dent insinuating that there might be a connection between him and the murders, due to the Waynes funding the Falcone Crime Family in the past. Bruce recalls an incident from his childhood where he met Carmine after his father saved his life following a shooting from the Maronis, and claims that this incident might've lead to the death of his parents a year later, insisting that any loyalty between the Waynes died with them.

On Father's Day, Maroni meets with his father, Luigi, who is then murdered by Holiday. Following his last advice of making peace with his enemies, Maroni approaches Dent, agreeing to testify against Falcone in exchange for prosecutorial immunity. On the Fourth of July, Harvey and Gilda watch the evening fireworks display on a boardwalk alongside Gordon's family. At the same time, Batman is captured while trying to stop Scarecrow and the Mad Hatter from robbing a bank for the Falcones, but easily escapes his restraints and defeats the two villains. At Carmine's signal, a mob hitman attacks the Dents. Catwoman intervenes but is in turn knocked unconscious by the hitman, who also knocks out Harvey when he gives chase under the boardwalk. When Harvey awakens, he finds the hitman dead, shot by one of holiday's guns, and hears a voice telling him to run before the police arrive.

Before Maroni's trial, Batman sneaks into Dent's house, finding paraphernalia associated with the Holiday killer in the basement, along with an Oxford pennant, presenting this evidence to Gordon privately on the courthouse roof. During the trial, Dent is tormented by more messages from the voice, and Maroni, going back on his deal, claims that Carmine is an upstanding citizen. Convinced by the Falcones that Dent is Holiday, Maroni throws a vial of acid in Dent's face to get revenge for his father's death, although he survives with horrible scarring. Waking up bandaged in the hospital, the voice confronts Dent again, and then takes over his body, escaping from the hospital after getting a phone call from Carmine. The call turns out to be a trap to lure Dent out to be assassinated for the Holiday killings, but Dent manages to kill the hitmen before being dragged underwater.

At Carmine's birthday party, he celebrates the supposed death of Holiday, only for Holiday to kill his sister, Carla Viti. Batman interrogates Gilda in order to learn more about Dent, still wanting to help him because of their friendship. Dent meets Solomon Grundy in the sewers and enlists the latter's help to attack the people who've wronged him, attacking the police convoy escorting Sal Maroni to prison. Batman, disguised as an officer, defeats Grundy and confronts Dent with Gordon, who has removed his bandages to reveal his scarred face and his new personality. Gordon accuses Dent of being Holiday, revealing the guns found in his basement, shortly before Maroni is shot by Holiday. Dent, seemingly having deduced who Holiday is, attacks both Batman and Gordon to keep them from giving chase to the killer, and then escapes with Grundy. Batman returns to Wayne Manor, which Alfred prepares for another Halloween, and begins to wonder what the point of his mission is if his parents helped create the criminals he fights; however, Alfred assures him that they would be proud. Dent and Grundy then attack Arkham Asylum, freeing numerous inmates, with the exception of Calendar Man. Batman begins to doubt that Dent was connected to the killings, citing the fact that he supposedly went to Oxford and never told anyone, and later asks Catwoman about her obsession with the Falcone family when she saves him from being shot by Carmine. She reveals that Carmine is her father, and she wants to find out her mother's name.

Dent and his associates begin to make their move, with Poison Ivy, Scarecrow and Mad Hatter attacking the streets, distracting the police to allow Dent, Joker, Grundy and Penguin to attack Carmine's building. Batman and Catwoman arrive, subduing most of the rogues. However, Harvey manages to shoot Falcone. Falcone's daughter Sofia runs into the room, picks up the pistol, and tries to shoot Harvey, but his gun had only two bullets. She falls out of a window. Catwoman catches Sofia, but Sofia lets go (probably due to the grief of losing so many family members) and falls to her death. When Catwoman unmasks herself, Falcone says the name, "Louisa.", which is probably Selina's birthmother's name. Later, Batman, Gordon, and Dent meet on the rooftop with the Batsignal. Dent confesses to all of the Holiday murders and surrenders to Gordon.

After Harvey is placed in Arkham Asylum, Batman visits Gilda. She tells him that she was the Holiday Killer. She was in a relationship with Alberto Falcone when they were students at Oxford. The Falcone family forced the two to get an annulment and forced Gilda to have an abortion, so she wanted revenge on the Falcone family. Gilda wonders if Batman will arrest her or tell Captain Gordon that she is the Holiday Killer. Batman only wants to know if she's done killing people and leaves without telling her his plans.

The movie ends with a scene at Wayne Manor. Bruce wonders why Alfred still bothers to leave candy for trick-or-treaters. Selina walks downstairs and teases Bruce. The doorbell rings. A family of three--two parents and a boy dressed as Batman--have come to partake in the holiday tradition.

In the post credits scene, the doorbell rings again. Alfred opens the door and sees The Flash and Green Arrow.