This a prequel story to Batman: Under the Red Hood on how Jason Todd died.
- Bruce Wayne/Batman (Bruce Greenwood) - protagonist of the film.
- Jason Todd/Robin (Vincent Martella) - impulsive successor of Dick Grayson.
- Joker (John DiMaggio) - the main antagonist
- Alfred Pennyworth (Jim Piddock)
- Comissioner Gordon (Gary Cole)
- Clark Kent/Superman (Kevin Sorbo)
- Sheila Haywood (Danika McKeller) - Jason's biological mother, she was killed alongside with Jason.
- Harvey Dent/Two-Face (John DiMaggio) - the secondary antagonist, who appears in Jason Todd's flashback
- Sharmin Rosen (Cindy Robinson) - a female Mossad agent who was one of the 3 possible identities of Jason's biological mother
- Lady Shiva (Janyce Jaud) - an assassin and one of the 3 possible identities of Jason's biological mother
- Ra's al Ghul (Jason Isaacs) - appears in the post-credits scene and was revealed to have been the greater scope villain behind Joker's killing of Jason
The story follows Jason Todd, the second Robin. His relationship with Batman has turned sour of late and his battles with criminals are almost suicidal. Batman decides that he turned Jason into Robin even before the boy had come to terms with the death of his parents. He therefore relieves him from duty. Jason resents this and storms out refusing to discuss the issue of his parents.
While walking through his old neighborhood, he meets Mrs. Walker, a friend of his parents, who gives him a box containing his father's old papers and other documents, including photos and articles relating to his family. Among them, Jason finds his birth certificate and a gut-wrenching surprise: the name of the mother has been almost blotted out (the contents of the box are a little water-damaged, due to Mrs. Walker's leaky roof), but the initial is "S", not "C" as in Catherine Todd, the woman Jason knew as "Mom".
He concludes that she was in fact his stepmother and resolves to find his biological one. Searching the box, he finds his father's now out-of-date address book which gives the name of three women whose first name starts with "S", and he tracks their present whereabouts using the Batcomputer. However, all three are based in the Middle East and Africa. Jason therefore runs away from home to find them.
Meanwhile the Joker has escaped yet again from Arkham Asylum, leaving a trail of death behind him. Batman discovers that he somehow obtained a nuclear weapon and will sell it to terrorists. He tracks him to civil war-torn Lebanon where he and Jason meet up. They foil an attempt by Arab terrorists to destroy Tel Aviv using a nuclear missile sold to them by the Joker. Sharmin Rosen, a Mossad agent who was at the scene, and whom Jason was tracking, denies ever giving birth in Gotham City.
Another of the suspected "mothers" is none other than Batman's old acquaintance Lady Shiva, whom they track down to a terrorist training camp. It is only with Robin's help that Batman overcomes her in a fight that proves almost fatal for him. Using a truth drug they get her to admit that she is not the mother.
They then go to Ethiopia, which is in the middle of a famine, and meet the third "suspect": Sheila Haywood, an aid worker. She proves to be the right one and she and Jason have an emotional reunion. However, unknown to Batman and Robin, Sheila used to perform illegal abortions in Gotham and has been blackmailed by the Joker into giving him the medical supplies her agency has in a nearby warehouse.
Not only is he denying the medical supplies to the starving in order to sell them on the black market, but the Joker also replaces them with his laughing gas which, once set off, will kill thousands of people.
Sheila herself has been embezzling from the aid agency and, as part of the cover-up, hands her own son (now in his Robin costume) over to the Joker. The Joker brutally batters him with a crowbar. Robin is soon lying unconscious in a pool of blood, which the Joker complacently remarks is "a bit messy". He then leaves him and Sheila in the warehouse with a time bomb.
Sheila and Robin try desperately to get out of the warehouse but are still inside as the bomb goes off. Batman arrives too late to save them and they die from their injuries.
The bodies are taken back to Gotham for burial. Since none of their relatives can be found, the only people attending the funeral are Bruce Wayne and three friends, butler Alfred Pennyworth, Commissioner James Gordon and his wheelchair-bound daughter Barbara, herself a victim of the Joker (see Batman: The Killing Joke).
Blaming himself for Jason's death, a guilt-ridden Batman resolves to carry on alone. He even turns down Alfred's suggestion to involve Dick Grayson, his original partner.
The Joker himself, meanwhile, has met none other than the Ayatollah Khomeini, who offers him a position in the Iranian government. The Joker leaves a warehouse filled with the dead bodies of his discarded henchmen and a clue in the form of a message painted on the wall in red paint reading B, See you at 42nd and 1st. J., which Batman realizes refers to city street corners. After eliminating Gotham City and Metropolis as possibilities, Batman discovers that on the corner of 42nd and 1st in New York is the United Nations building, which has to be what the Joker's message refers to.
While waiting outside the building, Batman meets Superman, who has been sent by the State Department. Superman tries to convince him to leave, and his evasive attitude and refusal to answer questions leads Batman to punch him across the jaw; fortunately, Superman rolls with the punch, leaving Batman with only badly bruised knuckles. Superman asks Batman about Jason, and at this point a limousine pulls up at the curb. The Joker steps out, revealing to Batman and Superman that he is to be Iran's representative at the UN.
Ralph Bundy, a CIA contact, tells Batman to keep away from the Joker since it could start a diplomatic incident, which the government would rather avoid. The Joker has diplomatic immunity and every crime he has ever committed has been swept under the carpet.
He is due to give a speech to the General Assembly and Bruce Wayne uses his high-level contacts in order to get in as an unofficial observer. The Joker appears dressed in Arab clothes and as he walks to the stage, he stops for a moment and exchanges glances with Bruce. Does he recognize Bruce as Batman? The question is never answered.
The Joker makes his speech claiming that he and the Iranians are treated with disrespect by the rest of the world. He announces that they will not take any more of such treatment and releases his deadly laughing gas over the Assembly.
However, a security guard breaks up the Joker's weapon and inhales all the gas, clearing the hall. It turns out to be Superman in disguise. He flies out of the building in order to get rid of the gas while Batman and the Joker fight it out.
The Joker gets out of the building and into a helicopter sent to him by his sponsors. Batman gets in and, during the fight that follows, one of the Joker's henchmen opens fire with a machine gun. The bullets fly everywhere, hitting everyone, including the Joker and the pilot, who loses control and crashes into the sea.
Superman saves Batman, who tells him to find the Joker's body; unsurprisingly, the archcriminal's corpse is nowhere to be found. Batman laments that everything between him and the Joker ends that way: unresolved.
In a post-credits scene foreshadowing Batman: Under the Red Hood,