Batman and Robin Must Die opens up with an iconic image that is slightly different than the one that everyone is accustomed to. It features Thomas Wayne as the surviving member of the Wayne family in the alley where his family was killed. This scene is all in Hurt's head, as he announces to Gotham that he is Thomas Wayne at a news conference. Hurt heads to Wayne Manor where Batman and Robin are subdued. He taunts Dick Grayson and apparently shoots him in the head as Damian looks on in shock. Three days earlier, Robin arrives at the scene where Batman is questioning the Joker. He informs the Joker that he knew who he was. The clues that were left at crime scenes, such as the Domino's were a giveaway that whoever left them knew that he was once Robin. The domino's represented the Domino mask that Dick once wore as both Robin and Nightwing . Gordon stops the interrogation and eventually leaves with Batman to the Bat-Bunker. On the way there they converse about the changes around Gotham, and how his men prefer him to the old Batman. Robin remains behind with the Police and the Joker. While in the Bat-Bunker Gordon learns that the Joker has asked for Robin. Batman warns that that would be a mistake. Robin begins questioning the Joker, who notes that he sounds like the Batman. Robin beats the Joker with a crowbar. Batman and Gordon race to the Police Station but are hit with a rocket launcher. The Batmobile crashes and leaves Gordon with an unconscious Batman, while Professor Pyg is set free.
Robin, back at the police headquarters, continues to beat the Joker with a crowbar. During this the Joker just laughs and states that he likes this Robin. In a nod towards the death of Jason Todd, the Joker makes a joke about bringing his own crowbar. The Joker somehow causes Robin to be poisoned by his Joker Toxin and makes for an escape. Pyg and Hurt converse as Hurt looks upon the Bat Box, noting he can't open it without destroying what's inside. Meanwhile Gordon is doing his best to protect Batman as they get swarmed by Pyg's people. The Batmobile begins to self destruct although he tries to override the process. Dick awakens beneath Wayne Tower with Alfred tending to his condition. Batman tries to call Robin but the Joker answers instead. Joker wants Black Glove and as result has Batman and Robin working for him. Alfred mentions preparing the cave and mansion as per Dick's request. Gordon has been taken by Pyg and Hurt and Batman goes after him. Gordon tells Batman not to untie him, but does so and knocks Batman out. Hurt taunts Joker, who is still holding Damian laughs, saying it's much too serious for him. He appears ready to release Damian into this "game."
Joker opens up a coffin with Robin inside, still alive. Hurt, meanwhile arrives at the Manor where Alfred apparently has been waiting. The city appears to be in mass chaos and Hurt takes advantage of this. Joker takes Robin and leads him towards the Manor. Robin attempts to break free and states he's only doing this for Batman. Robin is set loose and finds Gordon who has fought off whatever made him attack Batman. Robin tells him to take control of the city. Damian fights off a lot of attackers, but in the end is captured. He tells Batman he is sorry there were too many. We arrive at where the arc started, Hurt shooting Dick. He reveals that the bullet will not pass through his skull, instead, if left untreated it will cause a hematoma, he will be in a coma in less than twelve hours. He tempts Damian, saying that he can save Dick, but it will come at a price. Damian reveals that they know who Hurt really is, and that he shouldn't have returned. He reveals he did know Thomas and Martha Wayne. He intends to ruin the Legacy of the Wayne Family. He tempts Damian again, showing him the box and starts a ceremony of the Bat. Dick tells him to stall. A whistle is heard and it opens the box. Inside is written one word on a piece of paper. "Gotcha!" Dick and Damian punch Hurt and they reveal that this was a trap all along. A figure is shown in the shadows as Dick tells Hurt "Devil...Meet Bat-God."
The conclusion of the arc begins in 1765 in the middle of what appears to be some sort of ritual. A man, resembling Hurt goes apparently eats a bat and something changes in him as he talks with a creature that seems to be hinted at being Darkseid. The time shifts to the present, showing The Batman facing off against Hurt. Dick and Damian stand next to Batman, there are now two Batmen and a Robin. Damian questions if Bruce is a robot but they say they will talk about it later. The three fight off what appears to be an endless horde of attackers. Amidst the fighting Bruce questions why Dick is wearing the costume. Dick tells him that he had to because Jason Todd was masquerading as Batman. Bruce says they'll talk about his trip through time when they have some time. They deal with the swarm and Bruce asks him what they're dealing with. They let him know about what's going on and Bruce tells Dick he needs medical attention as soon as he can. Hurt is revealed to be Thomas Wayne, just not THE Thomas Wayne. He's from 1765 and the "black sheep" of the Wayne Family. Before sending Dick and Damian off, Bruce tells Damian he was proud of him and the choices he made. Hurt traps him in a tank that rises with water. Hurt tells him he'll never get out. "Batman R.I.P. Rot in Purgatory." Batman and Robin are going after Pyg, Damian pleads with him to stop and get medical attention. Pyg is brought into custody by Gordon. Hurt tries to reach "Barbatos" but his head is slammed into a mirror by Bruce. Hurt gives Bruce a choice, go after him or save Alfred. Batman saves Alfred while Hurt escapes, but is soon apprehended by the Joker, who buries Hurt alive. Batman later captures the Joker. Bruce see's to Dick and Damian. He tells Dick he is to be inactive for two months, Dick says something about Nightwing, but Bruce brushes it off. Damian asks what will happen to Batman and Robin. Bruce tells him "Batman and Robin will never die." Together, as a family Dick, Tim, Damian, and Alfred accompany Bruce Wayne to a press conference where he reveals that he has been funding Batman and that he plans on expanding the franchise globally. Batman Inc.. begins.