The Society and the League are called to Arkham Asylum, where Doctor Destiny is manipulating Dream Girl into creating horrific illusions. Starman manages to free her by saying "Lightning Lad" in Interlac. Dream Girl then reveals that there are other Legionnaires in the present. The JSA and JLA decide to team up and search for the lost Legion members.
Superman, Stargirl, Cyclone, and Red Tornado go to the Fortress of Solitude where they discover Wildfire, frozen among statues of various Legion members. (Superman has the statues because, for the first time since John Byrne's The Man of Steel (1986) reboot of the Superman mythos, he is described as a member of the Legion since his youth.) When Superman says "Lightning Lad", Wildfire unfreezes, and disgorges what looks like Batman's Utility Belt from within his body. At the Batcave, Batman, Starman, and Black Lightning talk to Karate Kid, who is insisting that he is a member of the Trident Guild, until Starman says "The Magic Words", and his memory is restored.
Jay Garrick, Vixen, Hal Jordan, and Tom Bronson, enter Gorilla City, where they find Timber Wolf and restore his memory. Meanwhile, Red Arrow, Power Girl, Hawkman and Hawkgirl head for Thanagar in search of Dawnstar, only to find that she has already left for Earth. The rest of the Legion members remove miniature lightning rods from the utility belt and proclaim "One of us has to die". Superman finds one of the rods, and realizes they planning a "Russian Roulette", just as they once did to restore Lightning Lad to life, though at the expense of one of their own.
The JSA and JLA converge at the old Secret Society of Super Villains base in Slaughter Swamp, looking for the final Legionnaire, who they believe to be Triplicate Girl, and are attacked by a rogue mechanism named Computo. As they battle, Superman realizes that he has been through a battle exactly like it before, and realizes it to be the work of Sensor Girl. Before anyone can do anything, she is rescued by her fellow Legion members, and they head into a lightning cloud.
While the Society races to stop the Legionnaires, intercepting each of their positions, Batman and Hal Jordan recognize them as the place Barry Allen gained his powers, the mansion where he appeared to Batman during the Crisis on Infinite Earths, and Titans Tower. Despite the Society and League's best efforts, the Legion's plan goes ahead, with Karate Kid being the one struck, only just surviving. Within the crater caused by the strike are Wally West, his wife Linda, and their two children, who returned by "riding" the lightning. The Legion return to the future, except for Starman, who says that he is needed, and Karate Kid, who is joined in the present by one of Triplicate Girl's bodies. In the 31st Century, Brainiac 5 dismisses Wally's return as a side effect, stating that they got who they wanted. A close-up of the lightning rod Karate Kid was using shows it to have someone trapped inside.
As illustrated in the special All-Flash #1 issue, at nearly the exact moment lightning struck the rod and Wally West returned with his family, then-Flash Bart Allen was killed by Inertia and the Rogues.
A follow-up storyline, Superman and the Legion of Super-Heroes (Action Comics #858-863) ties up some of the loose ends presented in this storyline (such as why the Legion never visited Superman again after the first Crisis).
It should be noted that the overall story arc was published thirty years after the first JLA/JSA/Legion crossover in Justice League of America Vol. 1 #147 October 1977 & #148 November 1977, where the teams fought against Mordru, and thus was something of an anniversary event.