Part One

An elderly John Constantine^{[lower-alpha 1]} sends Barry Allen on a "time trip" to key moments in his life, from gaining his metahuman abilities to a fight against the power absorbing android Amazo created by Dr. Anthony Ivo to his wedding with Iris West.^{[lower-alpha 2]} During the fight with Amazo, Superman gets injured and is aided by Barry and Green Arrow and is brought to Bruce Wayne for medical help.^{[lower-alpha 3]} In response, Bruce suggests to form a team with Barry, Clark, Oliver, fashion model Mari McCabe, and John Jones, who is now living on earth as a private detective. However, they fail to recruit Green Lantern.^{[lower-alpha 4]}

During a press conference to unveil the Justice League headquarters,^{[lower-alpha 5]} Amazo attacks the Justice League, as its original primary function to improve human life has been altered by Lex Luthor to kill anyone that is not human. With the League unable to defeat Amazo due to its ability to absorb and copy their abilities, Batman opines that an airstrike is the only way to destroy Amazo, but the others reject the idea. The Flash goes to Ivo, who reveals he has contracted a disease that ages him rapidly, and has been researching quantum energy absorption with Luthor to create Amazo using extraterrestrial technology in hopes to siphon metahuman abilities using them to find a way extend human life. Ivo sacrifices himself by having Amazo give up all the absorbed metahuman energy to Ivo. Batman deduces Luthor gave Ivo his disease to prompt his experiments which causes Amazo to turn against Luthor. With Luthor arrested by the police, Amazo returns the stolen powers to Superman, Vixen, and Manhunter before shutting down.

Meanwhile, Barry is sent by Constantine to a parallel Earth known as Earth-3. After a brief confrontation with his Earth-3 doppelgänger, Johnny Quick, he is captured by the Crime Syndicate – tyrannical criminal doppelgängers of the Justice League – and is taken to their Hall of Crime, where he is interrogated by Superwoman's lasso, confirming their deceased Luthor's theory of the Multiverse and resulting in the Syndicate, who have grown bored with ruling their Earth, deciding to plot a Multiversal takeover. Suddenly, an anti-matter wave threatens Earth-3 and, despite the Syndicate attempting to halt it, it manages to destroy the world. Quick sacrifices himself to allow Barry to tap fully into the Speed Force and escape Earth-3 before its destruction. Constantine soon explains to Barry that he witnesses the parallel Earths being destroyed as his punishment and that Barry shares the same guilt.^{[lower-alpha 6]}

On the day of Barry and Iris's wedding that was attended by Lois Lane, Harbinger recruits Barry, Oliver, Mari, and John Stewart / Green Lantern to a space station, where other heroes and super-powered people are gathered. Flash reunites with the Justice Society of Earth-2 who are old except for Wonder Woman, Superman, and a reincarnated Hawkman as he mistakes the Aquaman of Earth-146 for the Earth-2 version, but the latter corrects him as he is from an Earth that is completely flooded by the oceans and he has a harpoon for a hand, long hair, and a beard. Batman meets Robin of Earth-2 and learns of his counterpart's Earth-2 history as Robin of Earth-2 also introducing his Earth-2 counterpart's daughter Huntress whom he had with Earth-2's Catwoman. Superman meets his Earth-2 counterpart and learns of Earth-2 Superman's relationship with Wonder Woman after his Lois Lane died. Each one is here based on their skills, strength, and speed from across the Multiverse and have been gathered by Harbinger as ordered by the Monitor, an ancient Multiversal being. The Monitor explains that an anti-matter wave, which is capable of destroying an entire universe, threatens the multiverse. Barry's time-tripping inspires the Monitor to create massive vibrational towers on the remaining Earths that will allow them to phase through the wave and survive. However, the wave rapidly spreads before the towers are completed.

Barry uses his speed 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 antimatter wave to pass through the various Earths and dissipate, apparently saving the day. Barry is soon approached by the Spectre. The Spectre 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 gained his powers, and has an epiphany. Barry then appears as a vision to Batman when he was trapped in the Warlord illusion of Warworld, telling him to go back to before "the beginning". Barry then vanishes, seemingly dying. Back on the space station, the heroes celebrate their victory. However, Harbinger, who is revealed to be Supergirl, realizes that they might have changed history when she sees her friends from the Legion of Superheroes (including her lover Brainiac 5) begin to disappear, ending the first part on a cliffhanger.

Part Two

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Non-speaking cameos

Various DC Comics characters appear in non-speaking cameos throughout the trilogy. Part One includes Aqualad, Atom, Baby Crockett, Batwing, Black Canary, Black Condor, Black Lightning, Blackhawk, Blue Devil, Captain Atom, the Challengers of the Unknown (Kyle "Ace" Morgan, Matthew "Red" Ryan, Leslie "Rocky" Davis and Walter "Prof" Haley), Creeper, Doctor Mid-Nite, Elongated Man, Firestorm, the Freedom Fighters (Doll Man, Hourman, Phantom Lady, the Ray and Uncle Sam), Guy Gardner, Hawk and Dove, Hawkgirl, Jade, Katana, Max Mercury, Mento, the Metal Men (Gold, Iron, Lead, Mercury and Platinum), Metamorpho, Negative Woman, Nighthawk, Obsidian, Peacemaker, Red Star, Red Tornado, the Shazam Family (Lady Shazam, Shazam Jr. and Uncle Marvel), Speedy, Star Sapphire, Swamp Thing, Starman, Tempest, Thunderer, Wallace West, Warlord, Wildcat and Zatanna.