Set between 1953 and 1960, the film opens with an unknown entity (Keith David) narrating that it has witnessed the evolution of life on Earth and has decided to eradicate mankind because of its capacity of violence and destruction. At the end of the Korean War, United States Air Force pilot Hal Jordan (David Boreanaz) and his wingman, Kyle “Ace” Morgan (John Heard), are attacked by enemy pilots. Hal is shot down, ejects to safety and is forced to kill a North Korean soldier, causing him to be hospitalized for mental trauma. At Gotham Observatory, scientist Dr. Saul Erdel inadvertently teleports J’onn J’onzz (Miguel Ferrer)—the last survivor of the Green Martian race—to Earth. The shock of J’onn’s sudden appearance causes Erdel a heart attack. Unable to return to Mars, J’onn disguises himself as Erdel and takes his wallet and identification.
The following year, Superman (Kyle MacLachlan) meets Wonder Woman (Lucy Lawless) in Vietnam, where she celebrates the end of the war with a group of women. Wonder Woman allowed them to kill their captors, which horrifies Superman. Wonder Woman leaves America and returns to Paradise Island. In Gotham City, J’onn J’onzz has been living as Dr. Erdel while learning about human society through television. In Las Vegas, reporter Iris West (Vicki Lewis) is on assignment at the club where Hal Jordan and Ace Morgan are relaxing. While Iris is on the telephone to her boyfriend Barry Allen—known as Flash—(Neil Patrick Harris), Captain Cold (James Arnold Taylor) arrives to rob the club. Flash races to Las Vegas from Central City and confronts Cold, who tells him he has hidden six bombs around the city. Flash finds five of the bombs, deduces that the sixth is a decoy, and captures Cold, who is possessed by an unknown entity. Hal and Ace leave the club and head into the desert. They arrive at Ferris Aircraft, where a job as a test pilot is awaiting Hal.
J’onn joins the Gotham City Police Department using the name John Jones, and rises is promoted to detective in just two years. After investigating the kidnapping of a child as part of a sacrificial ritual for a doomsday cult that worships “The Centre”, J’onn and his partner Slam Bradley (Jim Meskimen) join Batman (Jeremy Sisto)—who is also investigating the kidnapping—in a battle against the cult, but a fire renders J’onn powerless until Slam extinguishes it. J’onn and Bradley free the child. The entity which possessed Captain Cold speaks through the incapacitated cult leader, identifies itself as “The Centre”, and warns of an impending judgment. Hal begins training exercises under Col. Rick Flag (Lex Lang) at Ferris Industries. Carol Ferris (Brooke Shields) recognizes Hal’s natural ability and tells him the real reason for his training; in response to Erdel’s contact with Mars and J’onn’s arrival, the U.S. government has commissioned Ferris Aircraft to build a spacecraft capable of traveling to Mars. Special agent King Faraday (Phil Morris) is assigned to oversee the project.
In Gotham, Batman reveals his knowledge of J’onn’s true nature, shields his mind from J’onn’s telepathy, and suggests they work together since they are both investigating a growing, worldwide, The Centre-worshipping cult. In Central City, The Flash defeats a robotic duplicate of Gorilla Grodd, but is targeted by government agents trying to capture him to learn the secret of his powers. Flash considers retiring from crimefighting; as he announces it on television he crashes a news report. J’onn interrogates former Ferris Aircraft employee Harry Leiter, apprehended for murder while under the influence of The Centre. During the questioning, Harry tells them about the launch to Mars. Leiter’s ramblings are confirmed when Faraday arrives to arrest him. J’onn briefly glimpses into Faraday’s mind and learns the truth. After watching the Flash announce his retirement on live television and seeing the contemptuous public response, a disheartened J’onn tries to stow away on the rocket to return home. Before leaving, he arrives in the Batcave and reveals that he has been aware of Batman’s secrets for some time, and gives Batman the last of his research on The Centre.
Faraday sees J’onn is seen on camera trying to board the rocket, confronts him and fights him on the launchpad. J’onn beats Faraday but saves him from the rocket’s exhaust. The rocket is damaged and malfunctions shortly after leaving Earth’s atmosphere. Hal wants to attempt a landing, but his co-pilot Flag reveals that the rocket is loaded with weapons of mass destruction, and he will not risk a crash landing. After a brief struggle, Hal is ejected from the cockpit and is saved by Superman. Flag detonates the rocket. Faraday holds J’onn J’onzz prisoner. On Paradise Island, Wonder Woman trains with Mala and they are attacked by the approaching Centre. Abin Sur (Corey Burton), the Green Lantern of Sector 2814, finds Hal. The destruction of the rocket Abin had been traveling in badly wounds him as he enters Earth’s atmosphere, so he instructs his ring to find a worthy replacement. Abin leaves his ring with Hal and tells him of The Centre, which he describes as a monstrous creature that fears humans and seeks their destruction.
In the Batcave, Superman and Batman review J’onn’s research and hear Lois Lane (Kyra Sedgwick) reporting that a giant pterodactyl is attacking Cape Canaveral. Superman arrives and quickly defeats the creature. Almost immediately, Wonder Woman’s invisible jet crashes and she warns Superman that The Centre is coming. Faraday befriends J’onn; having read Faraday’s mind, J’onn found that Faraday believes that one day the world will live peacefully. With his hope for humanity renewed, J’onn decides to help save Earth. The Centre, a massive flying island with an army of mutant dinosaurs to guard it, begins to attack the coast of Florida. The Flash, Green Arrow, Adam Strange, the Challengers of the Unknown, and the Blackhawks, arrive and clash with the soldiers on the base. Superman stops the conflict and the superheroes agree to cooperate. Superman reconnoiters The Centre but is swiftly defeated. Moved by Superman’s effort, the other superheroes and military forces band together. Batman is accompanied by Ray Palmer, and they plan to use Palmer’s reduction ray to destabilize the island. The heroes will distract The Centre with a frontal assault while Hal and Ace fly a bombing mission into the creature, leaving Flash to crisscross the island with the ray.
The aerial assault is nearly outmatched before the Blackhawks intervene, and a herd of rampaging dinosaurs ambushes Faraday’s ground forces. The Centre’s psychic force overwhelms J’onn and he is rescued by Faraday, who is captured by a dinosaur. As Faraday is about to be eaten, he grabs two hand grenades and pulls the pins. The dinosaur swallows Faraday and its head explodes, killing both. J’onn shakes off The Centre’s influence and he and Wonder Woman help turn the tide of the ground battle. Hal and Ace shoot their way into The Centre’s core but a hallucinogenic attack disorients them. The creature secretes a thick, red fluid that jams their weapons and almost suffocates them. Hal’s ring relays instructions from the Guardians of the Universe (Robin Atkin Downes) on its use. Ace detonates his payload and is rescued by Hal just before his plane explodes. The ground crew prepares to send The Flash to finish the creature; he races across the ocean, leaps onto The Centre’s surface, covers it on foot, and leaps into the ocean. The Centre begins to shrink, but realizing its imminent destruction it heads towards land to destroy the humans. Hal envelops the island in green energy then tows it into space where it explodes.
The world celebrates The Centre’s defeat. Many participants in the battle attend a ceremony. Their victory and display of teamwork change public opinion about superheroes. A montage of various heroes and villains, and the birth of the Justice League—set to the titular John F. Kennedy speech—is seen just before the film ends.