Author's Note: This story will be in outline form; it was an idea I had from years back, like my Venom outline.
The film opens up on Krypton years before its destruction. Jor-El has a machine, which he created, known as the Brain Interactive Construct, which he nicknames Brainiac for short, activated to monitor and thus predict any future activities within Krypton's solar system via complex calculations. But upon the day of its activation, Krypton is hit by a small meteorite which leaks out a strange radioactive substance that gives Brainiac sentience and free will. He calculates when Krypton will be destroyed, so using his own scientific knowledge of himself, he transforms himself into a humanoid and flies off of Krypton.
A few days following Brainiac's departure from Krypton, the planet is invaded by the forces of Apokolips, led by Darkseid, who is looking for the radioactive essence of the Anti-Life Equation, which he tracked to this world. Krypton's military forces are able to hold off Apokolips's forces long enough in time for the forces of the New Gods, led by the Highfather, to arrive and assist Krypton. This forces the remainders of Darkseid's fleet to retreat back to Apokolips. Jor-El briefly discusses what happened with the Highfather, and Highfather explains that the New Gods had somehow lost the Anti-Life Equation from their hold because of Apokolips, and Highfather vows to find the Equation before Apokolips does. Darkseid, meanwhile, similarly vows that nothing will stop him from attaining the Anti-Life Equation. Cut to the classic opening title sequence, which features clips from Superman Returns.
After the opening sequence, we cut to the present just after Returns, with Lois Lane and Richard White's wedding taking place, but Clark Kent isn't there among the witnesses. We then cut to a bank robbery in progress, run by thugs in armor suits who are part of the organized crime syndicate known as Intergang. Superman shows up and he battles off and defeats every member of Intergang causing the robbery, leaving their defeated forms for the police to arrest before he leaves in a rush to attend Lois and Richard's wedding.
Just as he, as Clark, shows up across the street from the church where the wedding is taking place, Lois and Richard walk out as husband and wife. In spite of his lateness, Clark is still invited for the celebratory dinner, where Lois confides in Clark to babysit Jason while she and Richard are off on their honeymoon in Niagara Falls. Clark agrees.
We cut back out into space, lightyears from Earth, where the remains of an alien civilization on a now-desolate planet are observed by the forces of the New Gods, who determine that whatever did this was obviously the same presence that had done this to other worlds for the past several decades. These forces of the New Gods get into a brief battle with arriving forces from Apokolips who are assuredly there to also investigate the remains of this civilization. We cut away mid-battle to find that Brainiac is now flying for Earth; it turns out that he is managing to survive in space by feeding off of electrical energy and information attained by alien civilizations; when he was consumed them, he leaves them to die, and goes off to find his next food source, which, in this case, is obviously Earth.
Back on Earth, the movie takes some time to develop its subplot between Clark and Jason as the former babysits the latter, during which time Jason realizes that Clark is his father (Clark was initially reluctant as he wondered how this would affect his relationship with his mother and Richard). After this realization on Jason's part, Brainiac arrives on Earth and begins to feed off of its electrical energy starting in Metropolis. Seeing this, Superman confronts Brainiac at Metropolis's power plant, where they engage in a brawl which ends with Brainiac barely escaping when he realizes that he cannot take on the Man of Steel without more sufficient power.
The film then cuts to Apokolips where Desaad, Darkseid's personal assistant, tells his overlord that their forces have located the source of the Anti-Life Equation on Earth, where Darkseid is sure that his fleet will be able to make it to before the New Gods and finally attain the Anti-Life Equation. With that, he decides to come along personally to oversee this operation.
Back on Earth, following his battle with Brainiac, Clark decides to spend more time with Jason, getting to know him as a father to a son and allowing him to control his growing abilities as a human-Kryptonian hybrid. One of Jason's acting-out-on-his-powers moments in the film involve him confronting a bully at school in order to impress a girl that he likes, which Clark is disappointed at. This soon puts on a strain between Clark and Jason that coerces the former to act out and return to the Fortress of Solitude just to calm down. But there, he finds Brainiac, who has just absorbed all of the data, information, and energy contained in the Fortress. The two of them engage in another fight that ends with Brainiac easily defeating Superman in combat. He is prepared to kill him off before the forces of Apokolips arrive and begin to invade Earth in their search for the Anti-Life Equation. Brainiac flees while Superman finds himself battling off these forces along with the unprepared militaries of the world. Jason, meanwhile, manages to just barely survive one of the divisions of Darkseid's fleet that is invading Metropolis, and he ends up helping several people go underground with him, including his Uncle Perry, the girl he likes, and the bully.
Amidst the battle, Superman decides to first save Lois and Richard off in Niagara Falls. He manages to save them and hundreds of other people by the Falls by destroying most of their starfighters there, which catches the interest of Darkseid, who is watching the overall invasion from orbit. Desaad asks him whether or not they should sic their secret agent against him, but Darkseid holds off on such a command, believing that even in the midst of the invasion, their agent could still be of use to them. So instead, he sends down Kalibak and his trio of Female Furies - Lashina, Stompa, and Mad Harriett - to personally battle Superman.
Superman confronts Kalibak and the Female Furies and battles them while simultaneously protecting Lois and Richard from their grasp. In the confrontation, Superman is able to kill all of the Furies, but Kalibak, not only seeing Superman`s durability but also by orders of Darkseid, escape back up into space. Superman then picks up Lois and Richard and flies them back to Metropolis so they can help Jason. Meanwhile, we cut to Brainiac who has managed to enter Metropolis`s sewer system after swimming all the way from the Fortress of Solitude, and upon emerging in the city, he confronts a few of Apokolips`s insectoid ground troops who deliberately seek him out. Brainiac notices this and kills nearly all of them, sparing the last one to ask why they want him. The soldier explains that it`s because Brainiac is infused with the radioactive energy of the Anti-Life Equation. Brainiac then kills the troop and manages to calculate a way to expel the radioactive energy from his being and coalesce it into a blazing, fiery crystal in the middle of a street. Brainiac finds that the removal of the Anti-Life Equation from his being hasn`t taken away his sentience or free will, and he decides to try to leave Earth, intending to allow Darkseid to take the Equation, uncaring of what he wants it for. However, given the forces of Apokolips invading, Brainiac is forced to stay on Earth in order to destroy any and all forces in his way. But this becomes more difficult for him when the forces of the New Gods arrive to combat Apokolips; the New Gods recognize Brainiac as a threat, and pursue him as a secondary target amidst their battle against Apokolips.
Superman arrives in Metropolis with Lois and Richard just as the forces of the New Gods arrive. The New Gods manage to ally with Earth`s remaining forces just as Darkseid finds that the Anti-Life Equation is on one of Metropolis`s streets, but is emitting a deadly radiation that will kill any living being upon its spreading throughout the city. The New Gods find this out as well and begin an immediate evacuation of the city. Superman manages to land Lois and Richard just outside the limits as he returns to save Jason and some of the others. He rescues Jason and the girl he likes, but Perry dies along with thousands of other civilians and military forces of Metropolis, the New Gods, and Apokolips. The loss of Perry White is a sad event for the Whites, and for Superman himself.
As the battle of Earth progresses between the New Gods and Apokolips, Darkseid and the Highfather come to figure out that the half-life of the Anti-Life Equation is only a few hours, after which the radiation will be non-lethal to known life. Superman comes by this knowledge from the Highfather himself who sees him as only too valuable of an ally, and after Highfather briefly but succinctly explains that Darkseid`s attaining of the Equation will result in his takeover of the universe, Superman becomes dedicated to stopping Darkseid; his goal will be to attain the Equation himself so that he can bring it to Highfather, who will keep it safe. So, after the radiation from the Equation crystal dies down, the main body of the battle of Earth takes place in Metropolis as the New Gods and the American military duke it out with Apokolips`s forces, and Superman grabs the crystal to carry it back to Highfather. But he is tackled to the ground by Richard, who turns out to be a sleeper agent of Darkseid`s who, years earlier, was inserted on Earth to replace the real Richard White, who is now dead. It turns out that Richard is really Kryptonian, and was brainwashed into serving Darkseid from birth; his parents were abducted by Darkseid for that very reason, as Richard served as an experiment who turned out to be a good investment.
Superman and Richard engage in a violent fistfight which ends with Richard winning and taking the Equation, flying away and into the upper levels of Metropolis. But Superman manages to unleash a wave of heat vision upon Richard`s direction, which destroys the crystal and unleashes an explosive wave of energy that marks the end of the Equation`s existence. Richard`s body crashes down near the feet of Lois and Jason, where he apologizes for lying to them before he dies. Lois is angered by Richard`s death, promptly blaming Superman for it, and Jason is similarly angered even as the forces of Apokolips retreat. Superman, however, doesn`t have time to try to console Lois and Jason as he also sees Brainiac flying away, unhindered by the beaten forces of either Apokolips or the New Gods. So he flies up and tackles Brainiac down to the grounds of Metropolis, where they engage in one last battle in the ruined streets of the city. Brainiac almost bests Superman, but the Man of Steel is able to counter Brainiac and destroys him by ripping him apart by the waist, ending the artificial life. Superman then collapses from exhaustion and his wounds.
Within the middle of the solar system, as Darkseid`s forces prepare to depart even with the New Gods chopping at his defenses, he decides to leave a solar bomb at the edge of the solar system, timed to detonate just after his departure. The bomb is self-defending, using turrets to blast away any vessels from the New Gods that intend to neutralize it in any way. Jason finds out about the bomb from overhearing communications between the forces of the New Gods, and seeing that his father cannot help in time, he decides to say goodbye to his mother as he reveals that he is Superman`s son. He then flies up into the air and out into space, where he super-speeds to the bomb faster than it can stop him. He manages to damage its turrets and push it just outside the system, where it blows up, taking him with it. Later, following the victory against Apokolips, who departed the solar system prior to the bomb`s blast, Superman wakes up, healed, and weeps with Lois when they find out what happened to Jason.
In spite of Jason, Richard, and Perry`s losses, Earth celebrates its victory as it seeks help from the New Gods to repair the damages done across the world because of the battle. During all this, Superman reveals to Lois that he is really Clark, and they mend their relationship, prepared to face the future without their son. Roll end credits.
In a post-credits sequence, Darkseid returns to Apokolips and immediately, upon seating himself on his throne, learns that there was a report from the explosion of the solar bomb. All they found was Jason`s body, and Darkseid smiles in delight as he says something along the lines of, `I know just what to do with him.` The film ends there for a possible sequel.
End Note: Leave a review explaining what you would have liked to see improved from the story provided in this outline please. :)