The film begins in 1953 with whom we later learn is The Centre explaining how it witnessed the evolution of the Earth and mankind. The explanation is shown being written and illustrated into a book titled "The Last Story" by a mysterious person who then proceeds to commit suicide. Then cutting to the Korean war where US Air Force pilot Hal Jordan and his partner Ace Morgan are attacked by North Korean fighters who are apparently uninformed of the cease fire just put into effect. Hal is shot down and parachutes down to a trench where a North Korean soldier is. He is attacked and is forced to kill the soldier by shooting him in the face. The event causes great trauma to Hal and he is placed in a mental hospital for the next two years.
It then cuts to Gotham Observatory where J'onn J'onzz is inadvertently teleported to Earth from Mars by a scientist. His arrival proved to be too much for the scientist and he died of a heart attack due to the shock of seeing a Martian. Being unable to return to Mars he adopts the guise of the scientist and goes out into Gotham City.
The following year, 1954 Superman goes to Indochina (Modern day Vietnam) to meet Wonder Woman who is celebrating with rebel women she freed. Superman is shocked to learn of Diana's and The Amazons moral and legal code, they allowed the women to exact their justice on their captors. Superman reminds her that the government already doesn't trust superheroes, which led to the disbanding of the Justice Society of America, the death of Hourman, and Batman being branded as fugitive vigilante who is now wanted by the government. Diana however states the she does what she feels is right and leaves for Paradise Island.
In Gotham, J'onn is living in an apartment under the guise of Dr. Erbel, mistaking a television for a source of information on Earth culture. While watching television he demonstrates his shape-shifting powers by becoming Bugs Bunny, Groucho Marx, and finally a detective like character. In Las Vegas Iris West is interviewing famous nightclub singer Buddy Blake at a casino where Hal Jordan and Ace Morgan also happen to be. Iris then goes to call her boyfriend, Barry Allen when Captain Cold breaks in. Hearing the events over the phone Barry uses his costume ring and becomes The Flash, racing from Central City to Las Vegas he confronts Cold who tells him there are six bombs hidden around the city. Zipping around the city Barry finds five of the bombs, zipping around the city a few more times looking for the sixth bomb he deduces that there is no sixth bomb. He then zips into the casino upstairs into a room and out the window, leaping into Cold's helicopter; knocking Cold down into a fountain along with himself. Before Barry could subdue cold he was possessed by an unknown creature who asks him why he is different from the "lesser beings".
Hal and Ace leave the casino and head into the desert to Ferris Aircraft where Hal is going to be tested as a pilot.
Back in Gotham, J'onn is now with the Gotham City Police Department, under the guise of John Jones. John quickly rises to the rank of detective within two years, mostly due to him being able to solve crimes by using his powers. After investigating the kidnapping of a child which he later determined was part of a sacrificial cult, John and his partner Slam Bradley encounter Batman who is also investigating the kidnapping. They join Batman in fighting the cult members, a fire starts rendering J'onn useless because fire is Martians only weakness. His partner slam puts it out with a fire extinguisher, Batman then attempts to cut the boy loose from his bonds, terrifying the child. J'onn arrives and calms down the child, then he and his partner cut him down. The same creature that possessed Captain Cold takes possession of the cult leader, identifying itself for the first time as "The Centre" and warning of an impending judgment.
While at Ferris Industries Hal begins his training under Col. Rick Flag Sr., his joking daredevil like ways don't agree with Flag but Carol Ferris understands Hal and recognizes Hal's natural ability at flying planes. She also informs Flag that Hal should know the truth of his training and his mission. She takes him to an enormous underground hangar, to a conference room with the project's leader, Special Agent King Faraday. There he tells Jordan that several years earlier a scientist named Dr. Saul Erbel contacted Mars and accidentally transported a Martian to Earth. He then informs Hal that the mission is a flight to Mars to determine whether or not the Martians pose a threat to the Earth.
In Gotham, Batman reveals his knowledge of J'onn's true nature in his apartment, as he has found a way to shield his mind from J'onn's telepathy. Suggesting they should form an alliance since they're both investigating the ever growing cult that is spreading across the world. His act of kindness towards the boy leads him to think that he can be trusted. He warns him however that if he were to betray he is fully aware of and would use his weakness to fire against him if he felt he had to do so.
Meanwhile in Central City The Flash destroys a robotic copy of Gorilla Grodd but is then attacked by a group of government agents including Faraday and Mademoiselle Marie. They fire off tear gas and then throw a net over Barry but he phases through it and escapes.
At the Gotham city police station J'onn interrogates Harry Leiter, a former employee of Ferris Aircraft who was arrested for murder while under the influence of The Centre. During questioning, Harry slips and mentions the mars mission, then Agent Faraday arrives to take custody of Harry. J'onn greets him and when he shakes his hand he reads his thoughts and goes into his mind, uncovering the truth about the mars mission. He then goes to a local bar and on teh television he witnesses The Flash announce his retirements as a hero, he leaves and heads for the Batcave. He reveals to Batman that he's lost his faith in humanity and is planning to sneak on boar the space shuttle bound for mars. His response to J'onn's statement is cold and brief, telling him that not everyone has the luxury of leaving Earth.
He then goes to Ferris Aircraft and attempts to enter the ship but is seen on camera by Faraday. He confronts J'onn and attempts to shoot him but J'onn beats him and as the rocket was about to launch he grabbed Faraday and landed on a platform, then collapsing right before armed guards showed up. The rocket is damaged and malfunctions several minutes into flight. Hal wants to land the plane as he is skilled enough to do so but his co-pilot, Flag won't risk it as there are weapons on board. After a brief struggle with Flag, he ejects him and Flag then proceeds to initiate the self destruct sequence. When he is falling towards the Earth Superman comes to his rescue and safely brings him back to down to Earth to the launchpad. Superman then confronts Faraday for treating J'onn differently just because he doesn't look like everyone else. He also points out to Faraday that J'onn could have left any time he wanted to but he decided to stay and that should teach him something.
On Paradise Island wonder Woman is training with Mala, telling her of how much America has changed since the war over ten years earlier. She replies back saying that the island has changed, many Amazons no longer want Hippolyta in charge. The two of them stop training when they realize a huge creature, The Centre is approaching.
Back at Ferris Aircraft, while Hal is in a training simulator, it begins to shake and a green glow encircles it and it starts to fly. It takes him out into teh desert where he finds a crashed spaceship belonging to Abin Sur, the Green Lantern of Sector 2814. He tells him in his dying breath that he has been chosen to become the next Green Lantern of Sector 2814. He mentions that his ship was hit by massive amount of yellow energy, likely caused by Hal's ship exploding and that he was forced to crash land on Earth and send his ring out to find the next worthy man to become his replacement. He leaves his ring with Hal and warns him of the threat that The Centre poses to mankind before dying.
In the Batcave, Superman and Batman review the evidence gathered by J'onn and Superman meets Robin for the first time. Superman asks him why the change in his costume and why the boy, he replies that he set out to strike terror in the hearts of the guilty not the innocent. As they talk they hear Lois come on over the radio, reporting the attack of a giant pterodactyl at Cape Canaveral, Florida. Superman flies to Cape Canaveral an quickly takes out the creature. Right after Wonder Woman's invisible plane makes a crash landing, its cockpit smothered in blood along with Diana. Before losing consciousness she warns Superman of The Centre's arrival.
Faraday and J'onn are now shown to be friends, occasionally chess with one another. J'onn reveals that he decided to stay because of the upcoming battle with The Centre and that he telepathically linked his with him on the platform before his capture. He found that Faraday believes that one day humanity won't live in a world with fear and hate. Being able to find that within Faraday renews J'onn's hope in humanity and decides to participate in the upcoming battle against The Centre to save the Earth. Before leaving with Faraday to Cape Canaveral J'onn adopts a new friendlier look and becomes a superhero calling himself the Martian Manhunter.
The Centre then begins its attack on the east coast of Florida, finally revealing itself for the first time. The Centre is massive island like creature with an army of mutated dinosaurs on it's surface. The threat draws the world's heroes including The Flash (Who was convinced by Iris to come out of retirement), Adam Strange, Green Arrow, the Challengers of The Unknown, and The Blackhawk Squadron who clashed with the soldiers at the base. The clash was stopped by Superman who wants cooperation between both sides. Surprisingly Faraday agrees and seconds Superman's proposal along with J'onn, who feels that the government and heroes should work together for freedom. Superman then heads out to attack the Centre but is shockingly defeated in a second, leaving the other heroes and soldiers shocked.
The rest of the heroes and soldiers decide to band together, to fight the Centre in honor of Superman. Batman then interrupts a meeting between Faraday, J'onn, Will Magnus and the Challengers in order to present Ray Palmer, a scientist known for his work on matter reduction. One of the Challengers argue that it's a waste of time, the technology is too unreliable, causing everything it shrinks to become destabilized. Batman points out that that's the exact point, everything it shrinks becomes unstable, meaning his invention could be used against the Centre. Ace argues that no could get fast enough to go over the entire island with the machine, Batman points out that The Flash is fast enough. Their plan is to distract The Centre with an air attack on the outside and a small two man team comprised of Hal and Ace attacking inside while The Flash runs across The Centre.
Together Batman in the Batplane, Green Arrow in the Arrowplane, and Challengers of The Unknown lead the air assault but are soon outmatched until the Blackhawk Squadron intervenes, though Faraday and the ground forces are quickly outnumbered as well as they find themselves up against an army of mutated dinosaurs. J'onn is then overwhelmed by The Centre's immense telepathic abilities, Faraday then comes to his rescue but is captured by a dinosaur. As he is about be eaten Faraday grabs an entire belt of grenads, pulling off two and then pulling the pins before landing in the creature's mouth.
The shock of Faraday's death helps J'onn overcome The Centre's psychic attack and then he and Wonder Woman help turn the tides on the battle. Hal and Ace shoot their way into The Centre and once entering they find themselves in a bizarre psychedelic world, disorienting them at first. A thick red liquid then starts to secrete from the creature, jamming the controls of their planes. Right before his plane is about to explode Hal's ring activates, along with a message from The Guardians instructing him on the use of his ring.
As Ace is about to detonate his plane Hal rescues him, now dressed in a costume identical to the one worn by Abin Sur. The explosion gives the ground force enough time to send the Flash in. Racing across he reaches the Centre in a matter of seconds and leaps up onto it, circling around the entire thing before leaping off into th ocean. As The Centre begins to shrink it heads towards the coast, to take humanity with it.
Realizing the destruction that will cause Hal uses his ring on it, enveloping the creature with his energy and then hauling it into space to let it explode. As the entire world begins to celebrate Hal celebrates the achievement of his goal, finally being able to fly through space. Amidst the celebration comes Aquaman or Arthur of Atlantis as he is called along with Superman who he says has been calling for a woman named Lois for some time. The heroes gather together for a photo by Jimmy Olsen of the Daily Planet, making the front page.