The story is framed around the journals of Carter Hall, who reveals a mystery that spans centuries revolving around divine metals that have landed on Earth. He gradually reveals a conflict that has existed since the beginning of time between four tribes: the wolf, the bear, the bird and the bat.
The Justice League is fighting Mongul on his war moon. When they return home, they find that Challengers Mountain, the headquarters of the superhero team called the Challengers of the Unknown, has mysteriously appeared in the middle of Gotham City. When they get into the mountain, they are met by Kendra Saunders, otherwise known as Hawkgirl, who warns them of a full-scale invasion. She proceeds to explain the concept of a dark multiverse, a multiverse that exists beneath the DC Multiverse, that contains a dark beast named Barbatos. Through her historical investigations into this creature, she has discovered a connection between Barbatos and the Wayne family. Batman is revealed to be part of a prophecy in which he will be treated by five divine metals that will open a door to the dark multiverse and allow Barbatos to invade the multiverse. It is further revealed that Barbatos first marked Batman when he was sent back in time by Darkseid’s Omega Beams during the events of the Final Crisis storyline. Despite this, Batman proceeds to steal Kendra’s sample of Nth metal, which is one of the divine metals. In bringing it to the Batcave to study it, the metal leads him to the journal of Carter Hall, which has been located in Wayne Manor the whole time. The journal confirms Batman’s suspicions regarding his role in the prophecy. He is then visited by Daniel Hall, who warns him that the “nightmare has only just begun.”
The whole Justice League searches for Batman. When Superman finds him, he interrogates him. During this exchange, Batman reveals that he has already been exposed to the foretold divine metals in a process called mantling. It started when he faced the Court of Owls and was exposed to electrum. He was exposed to dionesium during the events of the Endgame story arc, when he fought to the death with the Joker. The machine that was subsequently used to resurrect him exposed him to promethium. Finally, when he used the machine that allowed him to peer into the dark multiverse (during the events of the lead-up), he exposed himself to the Nth metal. In an attempt to escape the last metal, Batman steals Darkseid, who has been reduced to a baby. He aims to use Darkseid’s Omega Beams to go back in time again and prevent Barbatos from meeting him. Unfortunately, he is tricked by the Court of Owls and subsequently exposed to the last divine metal: batmanium. This causes him to exchange places with seven dark versions of himself from the dark multiverse.
Superman flies to the Fortress of Solitude where he encounters the dark versions of Batman for the first time as they introduce themselves as the Dark Knights. They all come from the Dark Multiverse—temporary negative realities created by the fears of people from their respective counterpart positive universes—and were recruited by Barbatos with the promise of preventing the end of their worlds. The Batman Who Laughs from Earth-22, who lost his sanity due to his world’s Joker, gathered the six other Dark Multiverse Batmen after they each had altered themselves to gain superhuman abilities. The Dark Knights’ membership includes the speedster Batman called The Red Death, a female amphibious Batman called The Drowned, a Green Lantern Batman named The Dawnbreaker, a cyborg Batman named The Murder Machine, a Batman known as The Merciless who wears the helmet of Ares and the Doomsday-infected Batman called The Devastator. Superman is overwhelmed as he is spirited away from danger by the Flash and Doctor Fate.
Superman meets the people who are left of the resistance, including those who are connected to the Nth metal such as Doctor Fate, Steel, and Plastic Man’s egg. Nightwing explains how major cities around the world have fallen to the dark versions of Batman. Suddenly, Mister Terrific interprets vibrations coming from Plastic Man’s egg, which indicate the coordinates of four locations that need to be investigated. Wonder Woman, Doctor Fate and Kendra Saunders go to investigate the Rock of Eternity. Green Lantern and Mister Terrific head to the remains of Thanagar. Aquaman and Deathstroke go to Atlantis. Finally, Superman has Steel and the Flash create a path into the Dark Multiverse for him through the Phantom Zone. Once he arrives, Superman realizes that it was a trap set by Dark Nights so they can harness the energy from his cells to power their doomsday device which would unleash their reality into the Multiverse.
While searching for the Nth Metal at the Rock of Eternity, Wonder Woman, Doctor Fate and Kendra Saunders face the personification of the Seven Sins. Kendra, entrusted with the mission given by the Council of Immortals, tries to fire the Anti-Monitor’s astral brain in the center of the Multiverse as an attempt to stop the Dark Multiverse, but is interrupted by Barbatos, who transforms her into a dark-hawk version of herself, named Lady Blackhawk. Meanwhile Dr. Fate is confronted by Black Adam, who alongside Vandal Savage, have brokered a deal with Barbatos. At the Outskirts of Atlantis, Aquaman and Deathstoke enter the sacred/ forbidden burial ground of Atlantis first king; Arion. Meanwhile, Hal Jordan and Mr. Terrific reach Thanagar Prime, where they find long-time Thangarian enemy Onimar Synn has conquered the planet with the help of JLA villain Starro. They have known of the Dark Multiverse’s existence for eons and have prepared to “raze the Earth” with a doomsday device called The Pheonix Cannon. Starro neutralizes Lantern and Terrific and the two are incarcerated.
As all this is happening, in the Dark Multiverse, Superman wakes Bruce from an unending nightmare. Overwhelmed by dark Supermen, the World’s Finest are saved by Daniel Hall. Taken to the Lucien’s Library in the Dreaming, Daniel proceedes to explain the history of the Multiverse, explaining that alongside the Monitor and Anti-Monitor, there is a third being; a “Forger” tasked to watch over what had yet to come. Within the Dark Multiverse is a “World Forge” which hammered out universes from the hopes and fears of all living beings (the most stable forming The Orrey of Worlds). Barbatos himself is a great dragon the Forger kept to destroy unstable worlds. Knowing only destruction, Barbartos killed his creator and the Forge began to darken (as twisted worlds survived). Convinced there’s still hope, Superman has him and Batman head for the Forge of Worlds. However, they find the Forge has gone dark, and are confronted by the Dragon of Barbatos; a corrupted Carter Hall.
Superman and Batman evade Carter Hall’s attack as they struggle to search for a spark in the darkened core of Forge.
Exiting a portal in Arion’s grave, Arthur and Deathstroke find themselves in the Earth’s core. Remembering a legend of how Arion saved Atlantis by using magic from the Earth’s core, they begin extracting Nth Metal, only to come under attack from Black Manta who’s allied with the Dark Knights.
At Thanagar Prime, Hal and Terrific are rescued from their cells by Martian Manhunter (who’s been exploring Thanagar Prime to learn about the secret Nth Metal deposits) and the trio proceed to rescue Plastic Man from Synn and Starro. However, they soon learn several Dark Knights have seized control of the Pheonix Cannon, reversing its polarity to make Earth sink further into the Dark Multiverse.
In the Rock of Eternity, Kendra regains control of her body after Wonder Woman uses her golden lasso on her, restoring Kendra’s memories, although she is still in her dark hawk form. Kendra decides to operate under her original alias, Hawkgirl, and arms herself with Carter’s mace. However, even after defeating Black Adam, both are beaten by the Batman Who Laughs, who explains that all the heroes have done is help accelerate Barbatos’ plans; Earth is now low enough for Barbatos’ army to claim the world. Refusing to give up, Diana and Kendra proceed to use the Rock of Eternity’s core to reach Barbatos and are confronted by the Dark Army of Barbatos.
Clashing their metals together (Diana’s Bracelets and Kendra’s Mace), the two heroines succeed in helping Green Lantern, Mr. Terrific, Aquaman and Deathstroke fight back against the Dark Knights, Terrific convinces Plastic Man to awaken, turning the tide of battle. Reaching the Dark Forge, Kendra manages to break Carter out of Barbatos’ corruption (reigniting the Forge in the process), Diana reaches Batman and Superman (donned in Tenth Metal, the prime constitute of the World Forge), and Barbatos is confronted by Flash and Cyborg, who have gathered reinforcements from other realities (including the “53rd Earth”).
Refusing to lose, Barbatos reveals his last resort; using the combined power of the positive energy of his prisoner Over-Monitor, the Anti-Monitor Brain’s negative energy, and Batman Who Laughs’ dark energy, he plans to destroy all of creation. However, an unexpected team-up of Batman and Joker halts this plan, the Justice League defeat the remaining Dark Knights and Hawkgirl subdues Barbatos. After Over-Monitor explains that all living things have trace amounts of Tenth Metal, the League proceed to use this power to pull Earth out of the Dark Multiverse (it also results in the Source Wall shattering).