Batman happens across a S.T.A.R. Labs truck hijacking. Batman makes short work of the trio of would-be thieves, insuring that the truck's cargo, an egg-shaped time capsule, reaches it's rightful destination, the Gotham Museum of Science and Technology. A thousand years later, two scientists, at a remote research installation, are marveling at a recent archeological discovery, an unhatched egg containing an anti-matter life form. Found amid the ruins of a dead civilization on Nandor, the "Mandoran Relic", as the egg is called, has a millennium long gestation period. While the egg is in no danger of hatching for some time, in the wrong hands it could be used as a horrifyingly powerful weapon. A single crack upon the egg could prematurely release the antimatter, resulting in a devastatingly destructive explosion. Enter Anton Halkor, a renegade cyberneticist, intent on stealing the Mandoran Relic. Halkor, however, is unaware of the presence of a Legion cruiser, in the vicinity of the research station. Quickly responding to the station's alarms, the Legionnaires storm the research installation. They find all the station's automated systems disabled, and the station guards all a catatonic trance. Spying a masked gunman, Cosmic Boy brings his magnetic power to bear. Though intent only on disarming the man, Cosmic Boy literally pulls the gunman to pieces, revealing him to be a robot. Checking on the Mandoran Relic, Colossal Boy and Sun Boy encounter another armed robot guard, one which Sun boy instantly melts into slag. The two young heroes rush Halkor, who turns and blasts them with a hypnotic ray, plunging them both into a catatonic state. Princess Projectra enters the room just as Halkor has finished cutting a hole in the protective casing around the Mandoran Relic. The fluid surrounding the egg is released in a high pressure stream that downs the Legionnaire. Halkor takes the Mandoran Relic, and vanishes.
Halkor reappears in 20th century Gotham City, specifically at the Gotham Museum of Science and Technology. Halkor leaves the museum guards in a catatonic state, then blasts his way into the vault holding the egg shaped time capsule.Halkor replaces the time capsule with the Mandoran relic. Halkor, however, is unaware that he has been observed by Batman the entire time. Batman crashes into the museum, through the skylight, and closes on Halkor. Batman takes out Halkor's hypnotic ray projector, with a well thrown batarang., then tackles Halkor. The two men struggle for several moments, until Halkor is suddenly drawn back to the 30th century, taking Batman with him. Halkor leaves Batman unconscious in an alley way, and reports back to his associate, Universo. Batman revives, immediately recognizing his surroundings. Batman heads to Legion headquarters to garner the assistance of the Legion of Super-Heroes. At that moment, honorary Legionnaire, Rond Vidar, is there, demonstrating a new model of his multiple time cube. Unbeknownst to the Legionnaires, Vidar is a pawn of Universo and Halkor's. Vidar activates his time cube, trapping Duo Damsel, Shrinking Violet, and Shadow Lass in various past eras. Vidar departs Legion headquarters with his portable time cube, and reports back to Universo. Batman and the Legionnaires compare notes, coming to the realization that the Mandoran Relic Halkor placed in the past, will reach the end of it's millennium long gestation in a matter of hours, resulting in an explosion that will devastate Metropolis. Batman figures on returning to the 20th century in time to stop Halkor from switching the eggs, until Chameleon Boy discovers that all of their chrononautic equipment has been sabotaged. Halkor breaks into the Legion's communications to claim responsibility for the disappearance of Duo Damsel, Shrinking Violet, and Shadow Lass. At that same moment, Princess Projectra confirms that Universo has escaped from Takron-Galtos, confirming the Legion's suspicions that Halkor's hypnotic technology was supplied by Universo.
The feint sound of dripping water, heard during Halkor's broadcast, is enough for Batman to determine where the renegade cyberneticist is hiding. Cosmic Boy, Sun Boy, and Colossal Boy lead a frontal assault on Halkor's lair, hidden in the sewers beneath Metropolis. Though the Legionnaires are quick to disarm Halkor, they are stopped short by Halkor's revelation regarding the fates of the missing Legionnaires. Halkor threatens to destroy the time cube, with a remote control detonator, stranding the missing Legionnaires in the past forever, unless the Legionnaires immediately surrender. Chameleon Boy and Element Lad ambush Halkor from behind, wresting the detonator from him. At which point, Batman beats Halkor into unconsciousness. The Legionnaires discover Vidar's unconscious body. Cosmic Boy tends to Vidar, while also taking Halkor into custody. Batman and the Legionnaires head to Gotham District Square to prevent the "time capsule" from being released on the street. Universo gets the drop on the Legionnaires, mesmerizing them into fighting against one another. With only three minutes left, Batman uses a laser torch to cut the Mandoran Relic from the time capsule's hydraulic platform, then attaches an anti-gravity device that sends it into orbit, where it explodes harmlessly. Rond Vidar jumps Universo, and the two men struggle on a rooftop above the battling Legionnaires. Vidar's time cube automatically returns the time-lost Legionnaires to Gotham District Square. Universo set the time cube to return them just as the Mandoran Relic detonated, in the hopes of slaying them all. Shadow Lass casts Universo in darkness, while Dup Damsel breaks up the fighting Legionnaires. When Vidar falls from the roof, Colossal Boy catches him. Shrinking Violet wraps Universo's cape around his head, then Batman beats him into unconsciousness. Vidar repairs a Legion Time Bubble, allowing Cosmic Boy to take Batman back to the 20th century.