Overlooking the universes of the five Earths on a floating asteroid, Alex and Lyla are joined by Pariah, who asks what part the Monitor could have intended him to play in the Crisis. Lyla responds that she has been told the Monitor's plan and knows what part he'll play in the conclusion, representatives of six Earths most these plans. Pariah obliges her by taking them to the merged Earths.

On Earth-S, where everyone has been freed of Psycho-Pirate's spell, Sivana and Ibac are about to be captured by Captain Marvel when, suddenly, they fade from the Earth-S plane. Captain Marvel Jr., Tawky Tawny, Changeling, Wonder Woman, and Supergirl arrive seconds later.

In space, Brainiac has drawn Sivana and Ibac to his satellite and greets them as the latest members of a select group who will soon rule the universe. Captain Marvel and the other-Earth heroes and heroines note that the wall of anitmatter has vanished. Lyla appears nearby, explains the machinations of the Psycho-Pirate, and enlists Captain Marvel as representative of Earth-S to hear the story behind the Crisis.

On Earth-2, Yolanda Montez, the new Wildcat, stands unseen above Green Arrow, the Atom, and Liberty Belle when she overhears Atom declare that there will never be another Wildcat. Yolanda realizes that she must prove herself worthy of the name before revealing her new identity.

On Earth-4, Pariah contacts its heroes and their former opponents from Earths 1 and 2. Blue Beetle will represent his Earth to hear Pariah and Lyla's stories.

On Earth-X, the Freedom Fighters pledge to Starfire to help all they can.

All five Earths are still slowly merging. however, and time still runs riot on all of them. Finally, Lyla, Alex, and Pariah stand on the asteroid, with Lady Quark, Superman of Earth-I, Uncle Sam, Captain Marvel, Superman of Earth-2, and the Blue Beetle. The heroes want to battle, but Alex and Lyla tell them that they must know exactly what they are fighting. Now, Lyla begins her story at the beginning—ten billion years ago when Earth was little more than cooling gases, the inhabitants of Oa, at the center of the universe, were immortal and had the powers of the legendary gods, and always strove for continued advancement, but their science became perverted, for one of them, Krona, swore to discover the secret of the universe's creation. Others warned him away, vowing that legends told of destruction to come to any who plumbed the mysteries of Creation. Krona called them fools, and continued his studies. He built a time-viewer in which he observed a cosmic Hand holding the galaxies in its palm. An instant later, a bolt of energy blasted the viewscreen and his laboratory to bits. Had Krona been mortal, he too would have perished, but that would have been far better than what actually occurred. At that point, according to Lyla, the Anti-Matter Universe was formed, and the single Universe split many times into a Multiverse. All planets of the cosmos were duplicated in every universe, save for one—Oa. Oa's sole twin was in the anti-matter universe. Its name was Qward. For his cosmic crime. Krona was converted to insensible, disembodied energy, and sentenced to circle the universe forevermore. Twice he managed to assume human form again; twice again he was defeated. The Oans, feeling responsible for Krona's actions, were consumed by guilt. They had created Evil, so they must form a force to constrain it. Their first attempt to do so was the construction of Manhunter robots, which later proved defective. Their second, and better, solution was the creation of the Green Lantern Corps. Still, there were dissenters among the Oans who maintained that evil must be destroyed, not contained. These dissidents broke away from the Guardians, and evolved into the Controller race, which would one day encounter the Legion of Super-Heroes. Oa and Qward had one moon each. On the moon of Qward, the Anti-Monitor broke the surface and came to life, repository of the power of a cosmos, and on the moon of Oa. the Monitor burst from a crater, symbol of the power of the positive universe. The Anti-Monitor quickly conquered the world of Qward and created the lightning warriors known as the Thunderers. The Thunderer elite he converted into his shadow-demon warriors, and with them he spread a reign of terror throughout the anti-universe. He hungered for more worlds to conquer, but did not know anything existed but the universe of Qward. At this point, the Anti-Monitor sensed the presence of the Monitor, who had spent his existence in meditation and study. The Monitor found his evil twin as well, and the two locked in combat for a million years. They were equal in power, so neither could win, but finally, both struck simultaneously and rendered each other unconscious for nine billion years.

Pariah now takes up the tale, explaining that he himself came from an Earth alien to them all, on which he was the greatest scientist, responsible for weather control and the destruction of disease. He soon discovered the existence of the Multiverse, and used that knowledge to learn the origin of the universe, despite the legends common to all planes that such knowledge would lead to destruction. He observed the creation while protected in an anti-matter chamber, but in so doing, he fulfilled the legend. A chain reaction of anti-matter destroyed his Earth, and then his universe. That cataclysm awoke the Anti-Monitor. The anti-matter universe expanded to fill the void left by the death of Pariah's universe, and he fed on its power. He realized that by destroying every positive-matter universe, he would gain all power in the cosmos. However, Lyla interrupts, the cataclysm also woke the Monitor, who vowed to fight back and protect the Multiverse. He viewed Pariah in an energy-globe learned what had happened, and deduced how the last survivor could be used to protect those who would stand at the end.

For mobility, the Monitor created his satellite-ship. He realized Pariah could sense where disaster impended, and they gave him the power to be drawn into other universes endangered by the anti-matter. But the death of each succeeding cosmos weakened him and strengthened his enemy. Then, the Monitor scoured all Earths to find heroes to act as soldiers in the Crisis, and so found her, a child adrift at sea, clinging to the remains of a sunken ship. He rescued her, raised her... and, she says, he was repaid with death. Superman of Earth-2 comforts her, saying they understand that she was being controlled, then asks Alex to tell his story. Before Alex can reply, Lady Quark must be restrained from killing Pariah. He is responsible for the force which destroyed her universe and family, she says. Uncle Sam demands she stop, saying that Pariah has suffered enough, and that they must now band together to save the worlds which remain.

The five Earths continue to merge, and all the heroes on them fear for their friends and allies who have joined the Monitor's aides in the war on the Anti-Monitor. Indeed, the Spectre maintains, not even his power would be effective in the anti-matter universe, but other heroes have been chosen: Mon-El, the Supermen of Earth-1 and Earth-2, Lady Quark, Captain Atom, Jade, Green Lantern of Earth-2, Wonder Woman, Captain Marvel, the Ray, John J'onzz, Wildfire, Firestorm, Dr. Light, and Supergirl.

Alex reveals his secret power: being composed of both positive and negative matter, he can open a portal between their multiverse and the anti-matter universe. Pariah can then guide them to their enemy. Alex then tears open a space-warp and admits the heroes and heroines into the universe of Qward. Finally, the heroes arrive at the bizarre fortress of the Anti-Monitor. They have been watched by their foe, who orders the Psycho-Pirate to make them emotionally controlled slaves. The Pirate, fearfully, tells his master that controlling the three Earths has exhausted his power, and he must recharge. The Anti-Monitor angrily knocks him down, and prepares to take charge personally.

In the fortress, the heroes search for their enemy. Abruptly, Pariah is gripped by a stony hand—the fortress wall, itself — but he is invulnerable to harm. However, Superman of Earth-2, is knocked reeling by another such hand. Monsters materialize from the walls and begin fighting the Monitor's warriors. The heroes can barely hold a stalemate, for these monsters, once smashed, can reform in seconds. Superman is in the forefront, searching for the Anti-Monitor while the others hold off the monsters. Pariah leads the way, with Dr. Light by his side. Suddenly, a thrusting trunk of stone seemingly obliterates Pariah. Dr. Light vows that the Anti-Monitor will pay for that death and blazes off. Superman catches up with her near a huge machine, which she identifies as a solar collector the villain is using to reduce the vibrational frequencies of the Earths, and thus merge and annihilate them. Superman vows to destroy it.

Then Anti-Monitor strikes Superman, and his cry of pain is heard by Supergirl, who heads to her cousin's side. Dr. Light attacks the enemy, but is rebuffed. He continues pounding the near-helpless Man of Steel. Racing to the scene, Supergirl passes Pariah, digging himself out of the rubble. The Anti-Monitor is about to kill Superman with an energy blast when Supergirl crashes into the villain with all her might. She delivers blow after blow, screaming, while Dr. Light looks on, inspired by her courage and selflessness. But the villain is too powerful. He knocks Supergirl back with a mighty smash, repulses her with a power-blast, and announces that he will kill Superman, and then her. Bleeding, she shouts that he will never kill Superman, and rips the floor from underneath him, causing his blast to miss her cousin. Then she pounds the enemy again and again, as the villain screams that she is destroying his life-shell. Dr. Light, watching, realizes the selfishness of her own life compared to Supergirl's, and announces that the Girl of Steel has shown him the true path. Superman, groggily, calls for his cousin.

The battered Anti-Monitor smashes Supergirl away again. His body has been almost totally destroyed by her pulverizing blows, and his energy is now waning. Super-girl goes to her cousin's side, and takes him to Dr. Light, telling her to take him to the others after she makes her move. Turning, she rockets into the Anti-Monitor, and sends them both into the massive vibration-reducing machine, turning it into scrap. She smashes at her foe's prostrate body, screaming that his scheme is over at last. Dr. Light is horrified by the combat, and calls for Supergirl to offer help. When Kara turns to reply, the Anti-Monitor grabs her with both hands and sends a titanic energy burst through her body. As Superman screams her name, Supergirl falls.

The Anti-Monitor, his body in ruins, shambles off to a portion of his fortress which is used as a spacecraft, and escapes. He needs time to heal, but he swears to stand triumphant "at the dawn of time." With his departure, the fortress begins to fall apart. Green Lantern of Earth-2 contacts the other heroes. Wild-fire reports that they have destroyed the merging-machine, but they've also had a casualty. Superman, holding his still-conscious cousin, begs her to live. Bleeding from many wounds, Kara tries to console him. He tells her that she ruined the villain's machine, and she gives thanks that she has given the Earths a chance to live. She asks him not to cry, tells him she loves him, and dies in his arms. Superman screams in anguish. He cries out for vengeance, but Superman of Earth-2 restrains him, telling him that Kara's sacrifice has given them a chance to save the five Earths, and his lust for revenge might endanger that chance. With the fortress coming apart, the heroes must leave. Superman takes Supergirl's body and follows his friends. Now empty, the fortress disintegrates. For the most part, the five Earths are for now out of danger. The time distortion has ceased, and the Earths remain linked, if not fully merged. Soon afterward, the worlds receive the news of Super-girl's death and a memorial service is held in Chicago. Thousands of people, including many super-heroes, and a grieving Brainiac 5, attend. Batgirl makes the opening address, praising her friend, while Lois Lane oversees the broadcast.

Later, Superman leaves his Fortress of Solitude with the body of Supergirl, wrapped in her indestructible cape, and sets her free in space, promising to remember and miss her forever.