Amanda Waller wakes up at 4:30 and checks her security systems. She then pours herself coffee and listens to the news as it reports a volcanic eruption on the Caribbean island of San Baquero. Waller calls for a car to go to her meeting, while the news talks about Luthor's announcement of a Presidential run as an independent. She then takes a shower and finds Batman waiting for her. Once she gets dressed, Batman reviews her history and Waller notes that she can find out his history if she wants. He dares her to do it, and asks what she's doing. Waller informs him that Superman had to tell the government about their battle against the Justice Lords to get Luthor's pardon. The government worried that the Justice League might go the same route as the Justice Lords, so she ran computer simulations and determined that the Justice League could win. They created Cadmus to produce the technology to defend themselves. When Batman warns her that he'll take her down if she threatens the world, Waller notes that the Justice League is the group with an energy cannon in orbit, and Cadmus are the good guys. Batman turns and goes, and a nervous Waller activates a security alert.
Aboard the Watchtower, the core members meet while other members help in the Caribbean. Batman reports about Cadmus and their development of weapons to combat the Justice League. Meanwhile, Waller meets with her Cadmus team. Hamilton assures her that Galatea will soon be back on duty, and the Doomsday project is almost ready. Tala is working to recover the Ares battle armor.
Flash figures that the Justice Lords went rogue because he died, and his team will be okay as long as they keep him safe. They're not convinced, and Superman wonders where the money is coming from to fund Cadmus. They figure that Luthor is involved, and Batman has sent the Question to investigate. Meanwhile, he's going to track the financing from Waller's end.
Professor Milo assures Waller that he's working to splice animal cells to humans, but Waller isn't impressed with his flawed program. She pulls his funding and agrees to set him up in a new non-vital capacity while confiscating his data. She warns that she'll be killed if he says anything. Milo imagines pulling out a gun and killing everyone, but leaves quietly. He goes to his lab and checks on Doomsday, held in power restraints. Milo is well aware that Doomsday is faking, pretending that the lobotomy that the Justice Lord Superman inflicted on him hasn't healed. When Doomsday remains silent, the vengeful Milo explains that Cadmus created him from Superman's DNA. They altered it to make Doomsday superior, then brainwashed him into hating Superman. In reality, it was Waller and Hamilton that inflicted mental and physical pain on him. When Doomsday became uncontrollable, they shot him into space via rocket. However, Doomsday broke free and it crashed back down to Earth. Doomsday then battled the alternate Superman. Milo is glad to explain that Waller betrayed them both, and Doomsday agrees to solve both their problems if Milo releases him. Milo does so and Doomsday solves his problem.. permanently. He easily slams his way past the guards and escapes in a travel pod.
On San Baquero, the Justice League and their support staff help the natives evacuate before the volcano goes up. The electromagnetic radiation prevents their radios from functioning, and Wonder Woman tries to contact Superman as he relieves pressure within the volcano by digging vent tunnels. As he works, Doomsday arrives and attacks him. Superman knocks him back and brings the ceiling down, but it's a temporary respite. Superman tries to explain it was his counterpart who attacked Doomsday, but Doomsday doesn't care.
Eiling and Waller confirm that Doomsday has gone after Superman, but Waller warns that they have to stop Doomsday before he goes berserk. She tells Eiling to take care of the problem. Once she leaves, he authorized a nuclear strike via submarine.
The League finishes evacuating the island and learns that Superman is under attack. Wonder Woman offers to help, but he tells her to continue the evacuation. She has no choice but to obey. Aboard the Watchtower, Batman and J'onn monitor San Baquero and detect the approaching missile equipped with liquid kryptonite. It's moving too fast for them to fire on it. Batman calls Waller on her Presidential phone and tells her to stop the missile. He warns that he'll come for her if anyone dies, and Waller say she'll do what she has to. She goes to confront Eiling, while Batman realizes that she didn't know about the launch. With no other hero available, Batman takes a Javelin toward the Caribbean to stop the missile himself.
Waller finds Eiling and demands answers. He points out they needed to take out Doomsday, Superman, and the drug smugglers on San Baquero, and that the anti-abort safeties are already in place. There's no way he can stop it.
Doomsday knocks Superman out of the volcano and smashes him to the ground. Meanwhile, J'onn notifies Wonder Woman about the missile. She tells Flash to take over the evacuation and goes to get Superman. Meanwhile, Batman catches up to the missile but is unable to shoot it out of the air because of its magnetic repulsors. J'onn tells him he can deflect it with an opposing charge using the Javelin. Batman manages to attract it to the ship's hull and pulls up just in time to avoid the island. He then ejects in a pod, leaving the missile to explode safely several miles away. The resulting tidal wave swamps Batman's escape pod and the island just after the escape craft escape.
Superman manages to use his heat vision to try and lobotomize Doomsday, but the behemoth can't be defeated the same way twice. The hero responds by punching him repeatedly, throwing him directly into the volcano. As the island erupts, Wonder Woman gets the weakened Superman to safety.
Aboard the satellite, the core League members convene and wonder what to do with Doomsday. His brain has been altered to make it resistant to telepathy, and Doomsday refuses to explain who created him. Superman has no choice but to use the Phantom Zone projector to banish him, and Doomsday warns that they'll wish they killed him. Once Doomsday is gone, Superman and Wonder Woman go to see the injured Batman. He accuses them of acting like demi-gods, passing judgment and forming an army. Superman insists that they would never do that, and Batman asks him what would happen if Luthor becomes President. He doesn't believe Superman's assurances and the two heroes leave. Batman contemplates a future with Luthor as President.
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