Aquaman and Aqualad pay a visit to Ocean Colony Alpha, to see what progress Dr. Larcher has made, in establishing the settlement. Meanwhile, an alien satellite crosses into Earth's orbit once more. The satellite is the last surviving relic of an alien world, long since vanished from the cosmos. Within it's structure lies a device that can open a dimensional rift in space and time. That device is triggered by Earth's magnetic field. The rift opens at the deepest point, in the cleft of an underwater canyon. Through the rift, Necrus, the so-called "Black City" emerges. Raiders from Necrus descend on Ocean Colony Alpha, slaughtering all the colonists and razing their structures. The lone survivor of the massacre makes his way to Atlantis, to inform Aquaman of the horrific attack. Aquaman and Aqualad immediately set off on their mounts, Storm and Imp, for Ocean Colony Alpha. Enraged at the brutality of the slaughter, Aquaman vows to bring Necrus down in ruins. Using his telepathy, Aquaman searches the seas for any marine life that knows the location of Necrus. At last, an aged sea tortoise appears, and leads the way to the "Black City".
As Aquaman and Aqualad approach the great dome, surrounding the underwater city of Necrus, they are met by the Cruel One. The two heroes retreat in the face of the awesome automaton. A tiger shark rushes in to protect the two heroes. The Cruel One fixes the shark in it's paralytic eye beams, then grasps it and begins violently shaking it. Aquaman and Aqualad engage the Cruel One to rescue the shark. Aqualad, too, falls victim to the Cruel One's paralysis beam. Aquaman shatters the Cruel One's ocular stalks with a broken piece of coral. Though blinded, the android still manages to grab Aquaman, in it's enormous pincers, and return with him to Necrus. Aquaman is brought before the tyrant king of Necrus, Mongo. Mongo is unrepentant regarding the destruction of the human colony. Mongo holds fast to the notion that surface dwellers have no place beneath the waves, and that the seas belong to those that already dwell there. Mongo proposes an alliance with Aquaman, and Atlantis, believing that if the two cities were united, they could easily wipe out all surface life. Aquaman refuses. Mongo entombs Aquaman within a crystal sphere, and casts him down a deep ocean trench, declaring that Necrus will now war with Atlantis. Aquaman witnesses the satellite's dimensional rift energy altering the shape of the coral, growing in the trench. In the hopes that it will somehow free him, he awkwardly maneuvers the crystal sphere into the very heart of the energy bleed. In Atlantis, Queen Mera is alerted to Mongo's armies closing in on the city. In Aquaman's absence, Aqualad marshals the city's defenses, and prepares to lead the Atlanteans into battle. Suddenly, Aquaman appears and takes command. Kissing his wife for luck, the monarch of Atlantis joins his forces, outside the dome, to repel the invasion force from Necrus. Mongo charges. Aquaman orders his forces to hold the line. When Mongo is seconds away from reaching Atlantis, Aquaman orders his troops to break formation, opening up a clear path for Mongo to lay siege to the city.
Before Mongo's forces can strike the shimmering dome of Atlantis, a squadron of swordfish raise up an immense net, that had lain hidden in the sea grass surrounding Atlantis. With Mongo's army entangled in the net, Aquaman orders the Atlanteans to close formation and begin beating Mongo's soldiers senseless. Mongo, however, is able to steal, unnoticed, into Atlantis, with his personal guard. They take Mera and her son hostage. Aquaman races in to confront Mongo, who orders the king's surrender, lest any harm befall his wife and son. Mera tosses Arthur, Jr. into Aquaman's arms, the better to bring her power to manipulate and control water to bear. Her hard water constructs take out Mongo's guards. Mongo flees, with Aquaman in hot pursuit. Aquaman grapples with Mongo. The Sea KIng is about to gain the upper hand when he suddenly, inexplicably, dies. All of Atlantis mourns the loss of their king. The royal funeral is attended by the Justice League of America, with Superman, Batman, Hawkman and the Flash serving as pall bearers. Mongo, in the meantime, has swam the long journey to Necrus, and has finally arrived home. He is stunned to discover Aquaman, still entombed within the crystal sphere. Releasing the monarch of Atlantis, Mongo demands an explanation as to how Aquaman could lead the Atlantean forces, while still a prisoner of Necrus. Aquaman offers no answers. A hard water fist relieves Mongo of his weapon, heralding the arrival of Mera, who is overjoyed to find her husband still alive. Aquaman explains that exposure to the dimensional rift energies had drawn a duplicate of the Sea King out of him, and outside the crystal sphere. Linked telepathically to his duplicate, Aquaman was able to direct it's actions, and even see and feel all that it experienced, including it's demise. Mera had suspected something was amiss when she had kissed "Aquaman", only to have the kiss feel strange and cold. The satellite breaks from Earth's orbit, and continues on its elliptical journey through the solar system. Outside of the influence of Earth's magnetic field, the satellite's dimensional rift projector shuts down, dispersing the dimensional rift, taking Necrus with it. Mongo is just able to make it back behind the walls of Necrus, before the "Black City" fades away. Aquaman is left to ponder the mystery of the ever shifting city, and to cope with "his" death, as life in Atlantis slowly returns to normal.