LexCorp's CEO Lex Luthor has been elected President of United States during a severe nation-wide economic depression. Under his leadership, the economy begins to thrive and he assembles a force of government-employed superheroes consisting of Captain Atom, Starfire, Katana, Black Lightning, Power Girl, and Major Force. Meanwhile, Superman and Batman maintain their distrust toward Luthor. The United States government discovers that a massive Kryptonite meteor is hurtling toward Earth. Instead of asking superheroes for aid and wanting to take credit for himself, Lex decides to destroy it with nuclear missiles. Lex arranges a meeting with Superman in Gotham City under the pretense of forming a pact. This results in a battle between the hired Metallo and Superman and Batman. Following the heroes' escape, Metallo is killed by an unknown assailant.
Later that night, Lex pins Metallo's murder on Superman, using footage of their battle to implicate him. Lex claims that the radiation being emitted by the meteor affects Superman's judgment, and he places a one-billion-dollar bounty on the Man of Steel's head. While breaking into S. T. A. R.
Labs, seeking information on the meteor, Batman and Superman find Metallo's remains and realize that intense radiation has killed him. They are then attacked by an army of villains looking to collect on the bounty. The army includes: Silver Banshee, Captain Cold, Icicle, Killer Frost, Mr. Freeze, Gorilla Grodd, Bane, Black Manta, Black Spider, Brimstone, Catman, Cheetah, Copperhead, Deadshot, Kestrel, King Shark, Brutale, Despero, Giganta, Girder, Lady Shiva, Mongul, Captain Boomerang II, Nightshade, Parasite, Solomon Grundy, and Shrike. After some effort, most of the villains are defeated. The remaining villains are defeated by Captain Atom, who has arrived with Lex's superhero team to arrest Superman.
All but Power Girl, whose loyalties are divided, attempt to capture the heroic duo. Superman creates a hurricane using his superspeed, and the two heroes escape with Power Girl. In Metropolis, Power Girl admits that she feels threatened by Lex, and doesn't believe Superman killed Metallo. Lex's superheroes catch up and the fight begins again, this time with Power Girl aiding Superman and Batman. The Dark Knight realizes that Major Force killed Metallo under Luthor's orders and goads him into admitting it in front of everyone.
In anger, Power Girl punches him in the stomach with so much force that it ruptures his containment suit. Captain Atom, ashamed at his complicity in Lex's misdeeds, absorbs the energy, disintegrating Major Force and injuring himself in the process. Meanwhile, Lex's missiles fail to stop the meteor due to the sheer amount of radiation being emitted. Amanda Waller discovers that Lex has secretly been taking kryptonite steroids, making him lose whatever rationality he had left. Lex decides to let the meteor hit the Earth so that he may rule what remains behind.
Batman and Superman break into Lex's lab to retrieve data on the meteor's radiation. They end up in battle with Captain Marvel and Hawkman, eventually emerging victorious with Power Girl's aid. Though Lex is unwilling to relinquish the data, going so far as to erase it from the lab computers, Waller gives them a copy. Batman and Superman fly off to Tokyo to submit the meteor's data to the Japanese Toyman. Waller tries to have Lex arrested, but he injects himself with more kryptonite steroids and dons a power suit. After escaping Waller and the military, Lex follows Superman and Batman. Toyman has built a rocket-propelled spacecraft, intending to use it as a powerful missile to stop the meteor. The ship resembles a giant, robotic composite version of Superman and Batman.
With the data, Toyman is able to calculate the necessary reinforcements needed for his own rocket so it won't explode before impact, as Luthor's missiles did. Lex arrives and disables the remote guidance systems. Batman volunteers to fly the ship himself, despite Superman's protests. Though initially faring poorly against Lex and his kryptonite power suit, Superman finally defeats Luthor in the streets of Metropolis in an aerial battle. Batman succeeds in destroying the meteor, and Superman finds him alive and well in an escape pod. With the truth of Metallo's death public knowledge, Superman is cleared of the murder charge and Luthor is arrested, all the while ranting that he, as President, cannot go to prison. Batman then returns to Gotham while the Daily Planet's star journalist, Lois Lane, arrives and she and the Man of Steel happily embrace.