In Smallville, Bruce, Clark, Diana, and Lois are having a small party with live music by Robin and Superboy. While waiting for the other guests to arrive, Bruce attempts to express his thanks for their help in the war they recently won. When it goes on a little too long, Diana jokingly cuts him off.
Before he can continue, they notice that he is bleeding…and that his blood formed a Bat symbol. Bruce manages to get out the words carpe diem before a giant hand erupts out of his chest and grabs Clark. Barbartos then rises out of Bruce’s corpse to everyone’s shock. Clark can’t understand how he is back after they just defeated him, and he explains that he let them win. As the Dark Knights ride in and kill everyone, Barbatos tells Clark that no matter what road he takes, they all lead to darkness.
Clark wakes up tied to Diana, seeing that he is bound to a giant tower in Metropolis. He recounts that while he was out, he lived through different scenarios where he attempted to fight Barbatos, but no matter who he recruited and what he tried, he failed. Diana says that she experienced the same thing, but what is happening in the real world is much worse. Tying themselves together with the Lasso of Truth to keep them sane, the two make their escape, until Clark sees dozens of civilians turned into Doomsdays. When he spots a turned Jimmy, he stops to help, but Diana forces him to keep moving. Diana explains the harsh reality; they were on the dark tower for seven days. During that time, Superboy made it to safety, but Lois was turned. Clark gets Diana to tell him where but Barbatos is, and he flies to Gotham to take him head on.
He arrives in Gotham and spots Barbatos atop a mountain. He tries to get to him, but stops when he spots Batman. However, it turns out to be The Destroyer, who knocks him into Crime Alley, now controlled by Mr. Freeze. The Batman Who Laughs is there to greet him, and he explains that while he is Bruce Wayne, he decided it was better to let Arkham’s inmates rule the city.
Superman tries to appeal to whatever good is left inside him. However, this Bat states that his Superman said the same thing before he murdered him and his family. As The Destroyer lays into Superman, The Batman Who Laughs explains that each world in the Dark Multiverse is created from the fears and hopes in the minds of beings from the standard Multiverse, using Destroyer’s history as an example. He also reveals that each Dark Knight wound up killing their version of Superman, which can be interpreted as Bruce’s fears or his hidden desire. Clark tries to counterattack, but because the Knights are made of dark matter, his punches don’t work. As Destroyer prepares to finish him, Flash appears and carries him through a portal to safety.
Superman regains his senses and sees Lady Blackhawk and what remains of the Earth’s heroes. Kendra explains that they are in one of the last safe places in the Earth-0 universe; the Oblivion Bar. Also present are Detective Chimp, and Nightmaster. Aquaman explains that Steel, Dr. Fate, and Mr. Terrific gathered them after their homes fell, but Clark is dumbfounded as to how everything got so bad in only a week. A battered Nightwing explains that they simply cannot stand up to this enemy. He reveals that even trying to reclaim only Gotham failed. On top of that, the The Murder Machine’s Alfred army is slaughtering Detroit; The Red Death has created a lethal Speed Force Storm over Central City. More cities fall by the hour, and a dark energy conductor is built in each one. Clark realises that Barbatos plans to drag them all into the Dark Multiverse, and tries to convince everyone to fight back. Nightwing explains that all who tried failed, including the Teen Titans.
Kendra interrupts to explain that the rescue gave away their position to the Knights. Diana believes there’s still hope, but Kendra responds because they refused to let her detain Batman, there’s no way to stop Barbatos. However, Green Arrow reveals what he learned in Gotham; Nth Metal can kill beings from the Dark Multiverse. However, Robin points out that Kendra and the Blackhawks destroyed it all. Dr. Fate explains that there a few sources of Nth Metal left, connected to the heavy metals on Earth. At the same time, Plastic Man’s body begins vibrating. Mr. Terrific translates the vibrations into coordinates pointing to four locations; deep space, Atlantis, the Rock of Eternity.
Diana suggests the remaining heroes split into teams, with one ally connected to the heavy metals on each. However, Arthur explains that Atlantis can’t be accessed, upsetting Hal. As they argue, Holt gets one last set of coordinates that are negative, and Clark realises they are in the Dark Multiverse.
He recalls that while he was connected to the dark tower, he sensed Bruce trying to communicate with him through his dreams. Kendra knows that Clark is planning to go after Bruce, and believes it is some kind of trap. Clark explains that he heard Bruce use the secret S.O.S the Trinity devised for urgent situations. Diana understands this, but still prefers to go after the Nth Metal.
Nightwing, even though he has felt Bruce call out too, votes that they leave him behind, enraging Damian. Dick believes that they cannot help him get out of the dark, and that Bruce would want them to fight the war in before them. Also, they only have three metal linked people and four locations. Before they can argues further, one of the Dark Robins arrives, but is subdued by the last metal-linked around… Deathstroke.
Before anyone can argue about working with Slade, the Bar begins shake, meaning the Dark Knights are arriving and they have to decide on a plan immediately. Superman resolves to not abandon Bruce, and gets Flash and Steel to help him venture into the dark in search of light. As the Dark Knights get closer, Dr. Fate and the metal wielders teleport everyone to one of the Nth Metal deposits. Kendra tries to convince Nightmaster to leave with them, but he decides to go down fighting, and the portal closes just as the Batman Who Laughs arrives. Kendra, Wonder Woman, and Dr. Fate arrive in Bialya and head for the Rock of Eternity. Hal, Mr. Terrific, and Plastic Man enter Sector 2682, nowhere near Thanagar. Holt explains that the Thanagar everyone is familiar with is an outpost, and the Nth Metal deposit is on their secret home world. Aquaman unhappily swims through the Mariana Trench with Deathstroke.
Finally, Superman, Flash and Steel are in the Fortress of Solitude, hoping to use the Anti-Monitor’s antenna to create a portal the Dark Multiverse. Clark explains his plan; he realised earlier that the coordinates in the Dark Multiverse are near the Phantom Zone. Using his projector to create a portal, then charging the antenna with Speed Force energy focused by Steel’s Nth Metal link, they should be able to get straight to Batman’s location. Hooking Steel up to the antenna and having Barry start running, the plan starts to work. Barry still has doubts that Batman is really reaching out, but Clark remains sure. On Steel’s signal, Barry hurls Clark into the Phantom Zone.
Meanwhile, the Dark Knights stand over a dead Nightmaster. As the Oblivion bar burns, The Batman Who Laughs has Dawnbreaker play a song on the jukebox. Even though it’s on fire, it still manages to play fine. As they listen, Clark breaks the barrier between the Phantom Zone and the Dark Multiverse, confident Kendra was wrong about it being a trap.
When he takes stock of his surroundings, he sees a dark tower shaped like an S, alerting Clark to the fact that it was a trap. Then, three decrepit Supermen subdue him, and he hears someone ask him why he came. It is revealed to be Bruce, almost completely drained of life. Clark explains that he got his message, but Bruce reveals that the message he picked up was Barbatos fooling him. The real message from him was hidden in the song from his last vision. The notes from the song the Super Sons played were ordered in the reverse of his emergency code as a warning not to come for him.
As The Batman Who Laughs toasts Clark’s defeat, it’s revealed that the final component needed to fuel Barbatos’ plan was the energy stored in Clark’s cells. As Bruce becomes engulfed in dark energy, he states that Barbatos was right about everything leading back to him, and that everything will now fall into darkness.