After Brainiac destroyed New Krypton with the help of Lex Luthor in Last Stand of New Krypton, General Zod seeks quick revenge and threatens to destroy Earth with the help of thousands of Kryptonians. Superman stands between his own people led by General Zod and his adopted home, Earth.
The War of the Supermen is divided into 4 parts (battles and issues):
- The Battle for New Krypton
- The Battle for Mars
- The Battle for Earth
- The Battle for Survival (or The Battle for Metropolis)
The Battle for New Krypton
At the beginning of the conflict, General Zod and Superman have an argument about who's guilty of attacking New Krypton. While Zod is angry and threatens to take revenge and fight all humans, Superman insists there is hope, and it was only Lex Luthor who was helping to destroy their home planet but not all people on Earth. Zod doesn't agree with Superman, who he believes should be on his side and not side with Earth. Zod orders his minions, Ursa and Non, to kill Superman with a Kryptonian knife but Superman manages to escape.
Meanwhile Alura is torturing Reactron, who is held captive after the previous events. While Supergirl is afraid of being complicit in a war crime and argue with her mother, Reactron starts laughing about the two arguing. He says he was meant to get caught. Alura notices something is wrong with the prisoner and pushes Supergirl into a containment vessel just in time before Reactron explodes, completely destroying New Krypton.
Shortly after the explosion General Zod declares war and mobilizes his troops.
The Battle for Mars
In the Daily Planet, Lois Lane reveals New Krypton is gone. Seconds later, Superwoman crushes into the newsroom and abducts Lois. Meanwhile Superman and Supergirl escape to Callisto, New Krypton's moon, where Supergirl starts crying while telling Superman it's all her fault because she brought Reactron into the prison. Superman tells her it's General Lane's fault because Reactron was one of his man, and Lane played everyone, even Brainiac.
In space, General Zod sends all Kryptonian troops towards the Earth's Mars Base and Earth itself.
On Earth, Jimmy Olsen gathers Superboy, Nightwing & Flamebird, Steel, and the Guardian to free Natasha Irons from the military base inside Mt. Rushmore and where she is held captive. Inside, General Lane welcomes his 2 daughters, Lois and Lucy. Lois is not amused by her father's actions though General Lane is convinced of doing the right thing.
On Mars, the battle starts, with Superman and Supergirl fighting alongside the Human Defense Corps and against their Kryptonian people. Only a few Kryptonians are engaged in the battle while thousand others continue heading towards Earth. Shorty before entering Earth's atmosphere, General Lane orders Lex Luthor to fire a special rocket, that combines the cadaver of a Kryptonian "God" with time-pool technology to turn New Krypton's sun into a red sun, thus heavily weakening Superman, Supergirl, and killing thousand of Kryptonians instantly.
The Battle for Earth
General Lane starts celebrating his success and Earth's victory while the group around Jimmy Olsen and Superboy crashes into the military base to free Natasha. With her information, the group is able to figure out the secret of Lex Luthor's bomb - using the corpse of the false Rao to change the sun. Flamebird immediately speed towards the red sun where they sacrifice themselves to destroy Rao and restore the sun.
General Zod, Ursa, and the remaining Kryptonians head towards Metropolis for the final battle. Supergirl and Superman, regaining their powers, rush to defend their adopted home. The Battle for Metropolis begins...
The Battle for Survival
Superman and Zod clash in Metropolis. Superman refuses to allow Zod to destroy humanity while Zod wants to turn Earth into the new New Krypton.
Superboy manages to recover the Phantom Zone Projector from the Fortress of Solitude and sends Non to the Zone as he attacks the Justice League.
Supergirl defeats Ursa and flies to the military base to confront General Lane willing to kill him and avenge the death of her people. While General Lane says here anger proves him right about Kryptonians he refuses to face judgment and apparently commits suicide.
When Superboy arrives at Superman's fight with Zod, Superman drags Zod into the Zone with him, willing to sacrifice himself to ensure that Zod is imprisoned for good. In the very last second Nightwing pushes Superman, his adopted father, back and takes his place, so Superman can continue defending Earth while he (Nightwing) remains in the Phantom Zone to ensure his biological father remains trapped, too.
Lois and Clarke are reflecting about the pointless war. Superman is uncertain if any Kryptonians have survived the war and are hiding somewhere on Earth. Lois is sorry for the Kryptonians' fate and promises to reveal the truth about her father's actions during the war despite the media portraying him as a hero for his 'defensive action', hoping that someday humanity will be ready for interaction with other alien races.
Note: In a first memo Lois mentions 'they called it "The Hundred Minute War" during which both sides suffered terrible losses.