In the 1920s, Bruce Wayne David Giuntoli travels abroad for twenty years after the murder of his parents, Darin De Paul Thomas Wayne and Martha Wayne, in search of answers behind the criminal mind. While investigating the disappearance of Cobblepot William Salyers's expedition crew, Bruce subdues an undead crewman, Grendon David Dastmalchian, who was freeing an otherworldly creature encased in ice. Bruce, his protégés Kai Li Cain Gideon Adlon, Dick Grayson Jason Marsden, Sanjay "Jay" Tawde Karan Brar, and butler Alfred Pennyworth Brian George retrieve Grendon and return to Gotham City, unaware that Grendon was infected with one of the entity's parasites, with Jay staying on the ship to watch over him.
Arriving at Wayne Manor, Bruce and his group are shocked to find the corpse of scientist Jeffrey Combs Kirk Langstrom in the library, as Bruce hallucinates a demon speaking through Langstrom’s voice. After he disposes of Langstrom's corpse, Bruce is visited by Jason Blood, the host of the demon Etrigan, who informs Bruce of a ritual which must be performed with his death, and the destruction of Gotham. Jason Blood Matthew Waterson warns Bruce of dangers tied to the city’s fate and the ancient powers that simmer beneath its streets.
Bruce, Kai Li, and Dick are later invited for dinner at hunter Oliver Queen's mansion. They also meet Harvey Dent Patrick Fabian, who tells them about Langstrom's obsession with the bats he had been studying. Donning a bat-themed suit of his making, Bruce (under the alias of Batman) investigates Langstrom's work at Robin's Row, which is related to the Cult of Ghul, a group who worship an ancient demonic deity, with the Testament of Ghul being the tool required for the ritual. Seeking the Testament, he stumbles upon cult member Talia al Ghul Emily O'Brien, who William Salyers Cobblepot’s rival, steals it to resurrect her father Ra's al Ghul Navid Negahban.
Meanwhile, Grendon manifests ice abilities and escapes, killing Jay, while Dick is killed by Killer Croc. While searching for Talia, Bruce discovers a book detailing a connection between Ra's and Iog-Sotha, an inter-dimensional demon with power over darkness.
Grendon then meets with Talia. It is revealed that the key to Iog-Sotha is the seed with which Grendon was infected. The seed emerges from his body, killing him in the process, and merges with one of Talia's followers to create a plant-like demoness, who scratches Dent and mutates half of his body into a portal. The demoness and Oliver fight and kill each other, with the latter entrusting holy weapons to Bruce and Kai Li before succumbing.
Bruce is met by detective Jim Gordon [John DiMaggio], who tells him that his daughter Barbara wants to meet with him. Batman goes to Arkham Asylum to see her and meets Thomas Wayne's spirit, who reveals his past. Centuries ago, he, Cobblepot, Langstrom, and Henry Queen established Gotham City, discovered the Testament in a cave, and used its magic to gain longevity and wealth as well as to bring prosperity to the previously barren land. However, this also woke Iog-Sotha and brought him to the threshold of their reality.
Bruce takes Oliver's weapons and the bottle housing Etrigan, bids farewell to Alfred, and leaves Kai Li in charge of the Batcave, before leaving to fight Talia. He kills Talia but is unable to stop Ra's, who is transformed into a powerful demonic creature. Bruce accepts his prophesied role as the Bat, transforms into a bat-like monster, and kills Ra's, but Iog-Sotha has begun to enter.
Seeing the bottle housing Etrigan, Bruce releases him and escapes the caverns as they explode, killing Dent, and Etrigan traps Iog-Sotha within them. Parts of Gotham burn and are destroyed, echoing Jason Blood's prophecy to Bruce.
Sometime later, Gotham slowly rebuilds and Bruce, Oliver, and Harvey are given memorials to honor their dedication and sacrifice to the city. Kai Li inherits Bruce Wayne's estate and fortune and promises to use the resources to help the city rebuild. As Kai Li delivers a speech in Bruce's memory to the public, Bruce — now permanently in his monstrous bat form — rests within Gotham's bell tower as he watches over the city.
