Part One Barry Allen experiences "time trips" from key moments in his life. One of these moments is a fight with the android
Amazo, during which
Superman (Earth-1) gets injured and is brought to
Bruce Wayne for medical help. In response, Barry suggests forming a team with Bruce, Clark,
Green Arrow, fashion model
Mari McCabe, and
John Jones, who now lives on Earth as a private detective. Amazo appears at the unveiling of the
Justice League headquarters, as its primary function to improve human life has been altered by Superman's archenemy
Lex Luthor to kill anyone who is not human. The League cannot defeat Amazo due to its ability to steal their abilities based on another member of Superman's rogues gallery,
Parasite. The Flash visits
Dr. Anthony Ivo, a scientist who has contracted
progeria and is dying. While researching quantum energy absorption with Luthor, Ivo created Amazo in hopes of siphoning metahuman abilities and finding a way to extend human life. Ivo sacrifices himself to depower Amazo. Batman deduces that Luthor gave Ivo the disease to prompt his experiments. Hearing this, Amazo turns against Luthor, but chooses justice over vengeance after the Flash's intervention. With Luthor arrested, Amazo returns the stolen powers to their respective heroes before shutting down. Meanwhile, Barry is sent by a mysterious man to
Earth-3, a parallel Earth. There, Barry is captured by the
Crime Syndicate – tyrannical doppelgängers of the Justice League – and is taken to their Hall of Crime. Using her Lasso of Submission,
Superwoman interrogates Barry, who confirms the existence of the
Multiverse. This inspires the Syndicate to plot a multiversal takeover, having grown bored with ruling their Earth. However, an antimatter wave then threatens Earth-3. The Syndicate attempts to halt it, but is consumed by the wave, which eventually destroys the world. Barry's doppelgänger
Johnny Quick, sacrifices himself to allow Barry to tap fully into the Speed Force and escape Earth-3 before its destruction. The mysterious man witnesses the parallel Earths being destroyed as his punishment and says that Barry shares the same guilt. On the day of Barry and
Iris West's wedding,
Harbinger appears. She recruits Barry, Oliver, Mari, and
John Stewart / Green Lantern to a space station called the Satellite. Harbinger has gathered various heroes and super-powered people from Earth-1 and several other Earths on behalf of
Mar Novu, a member of an ancient Multiversal race called the
Monitors. Flash reunites with the Earth-2 heroes, the
Justice Society, including their
Wonder Woman, Superman, and
Hawkman. Batman meets Earth-2's
Robin (
Dick Grayson) and
Huntress (Helena Wayne), the daughter of that world's Bruce Wayne and
Catwoman. When the
Legion of Super-Heroes member
Dawnstar is brought aboard, Harbinger reveals herself to be
Supergirl. Novu explains that an antimatter wave, which has been destroying universes, threatens the multiverse. Barry's time-tripping inspires Novu and his council of "thinkers" (consisting of Wonder Woman, Earth-1's
Doctor Light,
Hawkgirl, and
Mister Terrific, Earth-4's
Blue Beetle and
Question, and Earth-146's
Aquaman) to create vibrational towers on the remaining Earths that will allow them to phase through the wave and survive. However, the wave spreads before the towers are completed. Barry uses his powers to slow time for him and Iris, and they grow old together while completing Earth-1's tower with the help of Amazo. Upon completing the tower, the elderly Iris dies. The elderly Barry reverts to normal speed and activates the tower network by using a cosmic treadmill. The vibrational energy destroys his tower and Amazo, but causes the wave to pass through the various Earths and dissipate. The
Spectre then appears and claims that Barry bears responsibility for the Crisis, but that it is up to the Speed Force to determine his fate. Barry is then sent back to the moment he first gains his powers, when he has an epiphany. He appears as a vision to Batman when the latter was trapped in the
Warlord illusion of
Warworld, telling him to return to before "the beginning". Barry then vanishes as he dies. On the space station, Supergirl discovers that the Crisis has caused a
temporal paradox when she sees the Legion of Super-Heroes, including Dawnstar and her boyfriend
Brainiac 5, fade as the 31st century no longer exists, foreshadowing events that have yet to come.
Part Two When
Krypton was destroyed, Kara Zor-El's escape pod hits Novu's Satellite. Reluctantly at first, Novu rescued and took her in, feeding and educating her. When it became clear that Kara had lost her memory, he decided not to tell her of her home world's fate. Eventually, Kara discovered her escape pod in the Satellite's hangar and learned of her planet's demise. Enraged at Novu for refusing to prevent Krypton's destruction and withholding the truth, she goaded him to reveal that her cousin Kal-El was alive on Earth, prompting her to find him. Novu continued to observe her, including her training with the Legion of Super-Heroes. When Kara, now Supergirl, returned to Earth in search of Superman and Batman, Novu approached her to help him prevent the antimatter wave from destroying reality. He then gifted her some of his power, transforming her into Harbinger and sending her to gather the heroes. Years before on Earth-2,
Psycho-Pirate interrogated a codebreaker, his Earth's
Doctor Fate. To get Fate to talk, he explained his background. Believing that Psycho-Pirate had a role to play in the Crisis, Doctor Fate gave him the ability to travel between universes. After his plan to use the Atlanteans to attack the United States under the alias of Advisor failed, he used his new ability to leave Earth-2 and escape capture by Earth-1's Flash. He traveled the multiverse, trying and failing to take over various Earths, before being recruited by Harbinger and brought to the Satellite with the heroes. Time has passed since the antimatter wave hit Earth-1, and what was thought to be a single wave has turned out to be a series of antimatter waves. Many heroes are placed across the multiverse to operate, maintain, and protect the vibrational towers, while Novu's council tries to find a long-term solution. To keep the populations of the parallel Earths calm, they use the Satellite's technology to broadcast Psycho-Pirate's empathic control across the planets. Struggling with the mental strain of the task, Psycho-Pirate persuades Novu to give him some of his power to make it easier. Shortly afterward, Psycho-Pirate is abducted by an entity that is the polar opposite of Novu, the
Anti-Monitor, the source of the anti-matter waves. It offers him a new, smaller world to control in exchange for his service. After a weaker antimatter wave passes over the parallel Earths, shadow demons appear and attack all the towers simultaneously. Superman leads the Justice League to defend Earth-1, Batman defends Earth-2 with the help of a multiversal
Bat-Family that now includes
Robin (
Damian Wayne),
Batgirl (
Barbara Gordon),
Batman Beyond, and
Batwing, and Wonder Woman fights on Earth-46, an Earth ruled by
Amazons. Though they discover that the shadow demons are vulnerable to strong light, their attempts to fight them are undermined by Psycho-Pirate, who uses his enhanced abilities to heighten the heroes' hatreds and rivalries, causing them to turn on each other before he teleports them to another Earth. Due to the shadow demons and Psycho-Pirate's interference, not all of the towers are online when the next antimatter wave hits, and many Earths are erased, including Earth-46. Amid the chaos, a furious Supergirl murders Novu when Psycho-Pirate's powers exacerbate her resentment toward him. While defending Earth-1, John Stewart encounters the mysterious man who sent Barry Allen to Earth-3 and fights him. During their fight, the man remembers his identity as the sorcerer
John Constantine. As more shadow demons arrive, Stewart overloads his Green Lantern's battery, using it as a light bomb to destroy the shadow demons attacking Earth-1's tower. In response, the shadow demons coalesce into a single giant figure, revealing that the shadow demons were the Anti-Monitor's minions and are of one mind, which proves resistant to the heroes' light attacks. Powerless, they watch in horror as the Anti-Monitor prepares to destroy Earth-1.
Part Three When Novu died, he released the cosmic energy within him into the Satellite. This gave the heroes enough power to transport the surviving Earths and their Suns into a dimension between the universes called "the Bleed", preventing Earth-1's annihilation. Eight months later, Hawkgirl and Earth-2's Superman recover Wonder Woman's body in space, having survived Earth-46's destruction due to her immortality. While they are safe from the Anti-Monitor, the Bleed has different laws of physics; natural disasters occur daily; and beings from parallel Earths' past, present, and future have begun appearing all at once, straining their collective resources. After being exposed to
Scarecrow's fear gas while fighting Earth-10's
Nazi soldiers, Batman remembers an old man telling him to go back to before "the beginning", who he now realizes was a dying Flash. Doctor Fate confirms Batman's theory that the solution to the Crisis lies before the multiverse was created. Stewart tells the others about Constantine, who claimed to be from then. Batman, Fate, Stewart, and Wonder Woman leave the Satellite to find Constantine. Using Fate's magic to restore Constantine's memories, they discover that Constantine's Earth was ravaged by
Darkseid. To restore his Earth, Constantine instructed his Earth's Flash to travel back in time and kill Darkseid when he was vulnerable as an infant. Earth-10's Lex Luthor arrives on the Satellite, revealing that the Anti-Monitor has found the Bleed and forced its way inside. After it destroys Earth-146 and Earth-2, Question and Earth-1's
Lois Lane deduce that Luthor revealed the Bleed's location to the Anti-Monitor in exchange for Earth-10's survival. Luthor and his team of villains have correctly concluded that life in the Bleed is unsustainable, so they captured Psycho-Pirate and tortured him into contacting the Anti-Monitor. Luthor's true goal, however, was to bring the Anti-Monitor to the Bleed so that they could study its weaknesses, kill it, and return to the regular universe safely. After sacrificing Earth-AD to the Anti-Monitor to see its abilities in action, Luthor suggests that Earth-1's Superman could absorb the solar energy of all the Earths' Suns and channel it into a blast strong enough to destroy the Anti-Monitor. Despite knowing that this act would kill him, Superman agrees only for Supergirl to take his place while guilt-ridden over killing Novu. Returning to the universe, they are aided by a new
Green Lantern Corps and Martian Manhunter commanding the Warworld, who uses Psycho-Pirate to unite all the universes through hope. This energy blast weakens the Anti-Monitor long enough for Supergirl's sacrifice to obliterate it. As the heroes and villains gather on Warworld, Batman explains Constantine's role in the Crisis and that Darkseid was a fixed point in the universe, and the temporal paradox resulting from his death, instead of altering a timeline, shattered the universe into two halves, creating a reality with Darkseid and one without him. The multiverse has been dividing infinitely on similar decision points ever since. Because reality cannot cope with many universes, the Anti-Monitor was created as its
immune response, killing off universes to prevent its total collapse. A race of powerful beings that the Anti-Monitor belonged to approaches the Satellite and begins destroying
Earth-508,
Earth-12,
Earth-2003, and Earth-10, forcing everyone to see the futility of their efforts and the need to correct Constantine's mistakes. Constantine suggests fusing the multiverse into a single "Monoverse" that reality could cope with, and
Batgirl suggests using Superman's enemy
Brainiac's Miracle Machine, which Supergirl had hidden in a pocket dimension before she died. After
Nightshade teleports the Miracle Machine to Warworld, Wonder Woman sacrifices herself to provide immortal energy to recharge the machine and create the Monoverse, where the survivors will merge with their counterparts of that universe once they enter with no memories of their lives before the Crisis. Watched on by the Spectre, the assembled heroes and villains walk into the Monoverse except for Question, who rejects the "false reality" on principle, and Psycho-Pirate, whose mind was damaged to power Warworld, has left to die. Though Constantine braces himself for the Spectre's punishment for ending the multiverse, the latter offers him "hope" instead of "justice". As the Spectre leaves, Constantine considers following everyone, only to instead decline and accompany the Spectre to an unknown fate as the multiverse is ultimately destroyed. In the Monoverse at
Themyscira, a young Diana (this universe's future Wonder Woman) plays on a clifftop. Her mother
Hippolyta urges her to step away for safety, implying that the girl would not be burdened by immortality like Earth-2's Wonder Woman. ==Voice cast==