Superman tears through Toyman’s army and discovers that the villain has become part machine. Toyman informs him that Brainiac has control of all the world’s nuclear weapons; Superman leaves to stop their detonation. Batman and J’onn gain control over Luthor and Grodd under control; the heroes give Grodd the Weaponers’ Ring so that he might provide assistance.
The Justice League and their allies are trying to calm down the crowds of people driven mad by Scarecrow’s fear gas when Superman rejoins them. Supergirl, Red Tornado and Green Lantern blow away the clouds of hallucinogenic gas flooding the battlefield, but Scarecrow has taken advantage of the chaos to slip away. The heroes can’t waste time searching him, though. Brainiac has shifted his primary program to another body, and Superman deduces Black Manta has teleported away with Aquaman’s son. And they still have to stop a nuclear holocaust.
The heroes have to split up: Superman, Zatanna and Red Tornado will chase Brainiac down. The rest of them will divide and evacuate the cities under control of the Legion. Supergirl and her strike team head to Poison Ivy’s city. Wonder Woman and her team will go to Cheetah’s city, even though she’s little time left. The Marvel family get the children out of Toyman’s city. And Aquaman will go to Black Manta’s city to rescue his son and everyone else.
Scarecrow runs into the sewers, and is attacked by the Joker, who wears a Dracula costume.
Wonder Woman and her group – Batgirl, Plastic Man and Flash – make their way to Cheetah’s city. They sense they’re being hunted, and Wonder Woman stays to deal with Cheetah as her teammates evacuate the people. Cheetah attacks Wonder Woman. Diana removes her armour, displaying her deteriorating frame: the parts of her body are held together by her magic lasso. She declares Cheetah cannot hurt her further, and her ex-friend has run out of second chances. Diana takes down Cheetah, but she’s dying.
Superman, Red Tornado, and Zatanna pursue Brainiac, but he teleport s from place to place one step ahead of them.
In Poison Ivy’s citadel, Supergirl’s team’s progress is impeded by Ivy’s plants. Ivy tuns up, complaining they’re trespassing. Supergirl retorts with a burst of heat vision. Once defeated Ivy, Supergirl, Green Arrow, Black Canary, Elongated Man and Metamorpho hasten to get the people out of there.
J’onn links Luthor’s brain to Grodd’s and the three work to redirect the missiles.
Aquaman finds Black Manta and his son, and destroys the machine Manta uses to control his people. Aquaman defeats him and saves his son.
Luthor escapes and teleports to Brainiac; Superman subdues Luthor with the help of Zatanna, whose spell prevents him from teleporting away. They pursue Brainiac. Superman and Zatanna appear in space; Brainiac has shrunk his ship to avoid detection. Superman freezes the ship, wraps Zatanna in his cape, and darts to the earth’s surface in order to save her from the vacuum of space. Performing CPR, he saves her.
As Hal Jordan’s ring runs out of charge, the Green Lantern Corps arrives and gathers up all of the missiles. Hal’s ring removes the knowledge of the heroes’ secret identities from the minds of the villains.
On Paradise Island, Diana’s mother, Queen Hippolyta, prays to the gods to restore life to her daughter. Diana’s body fades into the Earth and a new body emerges out of the clay. Diana rises, her life renewed.
Joker and Riddler return to Arkham; Batman reflects on the changes they’ve made to the world, and opines that perhaps someday the world really will be made into a better place.
The Legion of Super-Heroes watch through time as Superman changes into Clark Kent and heads into the Daily Planet building.