The astronauts on the space probe make their way across the moon’s surface and enter the Watchtower and confront the Justice League, revealing that they are being controlled by the Bloodlines Parasites which in turn have granted them super-powers that the Justice League has lost. Against Batman’s wishes, Tommy begins shooting them so that he and the League can escape; during their rush to the elevator, one of the parasites attaches itself to Batman.
Based beneath Aquaman’s tank, the League take stock of their options and find that they couldn’t remove the parasite attached to Batman as it would kill him. A debate about whether or not to use torture tactics goes on between Flash and Green Lantern before Tommy takes the chance to shoot the parasite. Wonder Woman determines the parasites are a subspecies of the ones that invaded during the Bloodlines incident but more intelligent. Their possession causes a brief coma state before rewiring the host DNA and triggers a metahuman power. The aliens didn’t steal the Leagues’ power but instead developed a power to block their ability to use them. Their plan was to gain control of the League and use the teleporters on the Watchtower to travel to the Earth to assume the task of genocide while a breeding population would be established on the moon.
Wonder Woman reasons that as warriors, and with Green Lantern and Flash powerless, she and Tommy should attempt to regain control of the Watchtower’s communications and summon help from Earth’s superheroes. Wonder Woman and Tommy begin the arduous task of climbing to the communcations level. Soon after they are attacked by a group of the parasites and Tommy is forced to go alone as Wonder Woman fights back. As Tommy reaches the communications level, he is greeted by Superman who has been taken over by one of the parasites.
On Earth, the United States President reluctantly agrees to launching nuclear missiles at the Watchtower following reports that the League may have been infected.
Back on the Watchtower, Tommy helps Superman overcome the parasite which renders him almost powerless, leaving Tommy to face the remaining parasites. He shoots them and convinces the parasites to leave. The League members regain their powers and manage to call off the attack that the President had ordered. With the League restored, Batman hauls Tommy back to Gotham and hands him over to the police; however, the cops releases Tommy in lieu of gambling debts.
Clark Kent ends his story by explaining why Superman and the League worked with Tommy. He suggests that Tommy’s story might just be one worth telling. Before Kirby leaves he tells Clark that despite all of the superheroes being something of a joke in Noonan’s and Tommy would agree, except for Superman, who was always okay by him. Later Superman flies to the Watchtower and visits his one memorial to Tommy: the section of bathroom where the Hitman had written, “Tommy Was Here.”