Main characters in seasons three through nine of Legion of Superheroes.
Superman/Clark Kent - After the fight with the Joining, Superman was flying around musing about how he missed his friends from the future, though happy with his friends in the present, unaware he was being watched by Brainiac. Superman was brought to the 31st century again when the Joining began attacking. Superman always greeted Nightwing, noting his interesting family history. Superman then confronts new Super Droids with the Legion. Superman defeats his droid by punching it through the chest, so that it short circuits. After all the droids were defeated, Superman decided to make good use out of them by rebuilding them as guardians of the Fortress of Solitude. Superman then welcomed Kell back to the team when he returned due to a lack of need for heroes in the new 41st century. Superman then reveals that he's going to hang out with his old friends for a little bit.
Superman X/Kell-El - With the 41st century returned to its peaceful existence, Kell returns to the 31st century to help out there. He's then greeted by several other members including a returned Superman and the newest member, Nightwing. Kell was with the team when Ayla went missing, and he was surprised when Nightwing arrived, learning he was a descendant of Dick Grayson. Kell then went with the team and fought several of Dr. Londo's monsters until they arrived at his lab with a now teenaged Ayla. He was also surprised when Dr. Londo disappeared shortly after Ayla was freed.
Nightwing - A descendant of Superman, the original Nightwing, Starfire, and Raven. He was active for a year before following his nemesis, the Jester, to New Metropolis where he met Legionaries, Cosmic Boy, Lightning Lad, Saturn Girl, and Chameleon Boy. Nightwing turned down Lightning Lad's offer to help and continued to fight Jester, using his mental abilities to shield himself from a Kryptonite ray Jester had and destroy it. Nightwing then called Saturn Girl's kick that stopped Jester nice. Nightwing then explained himself to the Legion, at first resisting joining the Legion until Lightning Lad pointed out that they'd be able to help each other protect each of their homes. Nightwing eventually agreed and became a member of the Legion, including taking the Oath. Nightwing then took the Legionaries to the rebuilt Wayne Manor and showed them the Batcave, having gotten it from New Gotham PD in exchange for the recommission of the Bat-Signal. As a sign of good faith, Nightwing shared a flash drive with the Legion that held all the information from before the Great Crisis, made by Batman. When Nightwing saw Brainy get captured by Alexis Luthor a short time later, Nightwing commented on how that would be difficult. Nightwing then asked Computo for the location of the closest LangCorp building was. Nightwing then hopped down on Alexis, promising to liven up the room. Nightwing then went to release Brainy before Alexis trapped him in red sunlight energy. Relying on his Tamaranian DNA, Nightwing destroyed the laser with a Star Bolt. After Brainy was freed and Alexis disappeared, Nightwing knew something was up. When an odd energy signature attacks, Nightwing instantly recognizes it as the Joining. Nightwing then states that they'll need help when Brainy leaves and comes back with Superman. Nightwing refuses to get to know Superman for security reasons and coordinates an attack against the Joining and rebuilt Super Droids. Nightwing ended up facing a Batman-Droid that strategized around the droids' usual weaknesses. Eventually, Nightwing's able to short-circuit his droid by punching it in the chest. After this, Nightwing meets Kell and accepts him as a new team-member. When Ayla went missing, Nightwing insisted that they go with Lightning Lad. At Londo's lab, Nightwing freed a now teenaged Ayla from her restraints and assured her that she was safe.
Cosmic Boy/Rokk Krinn - Three years after the fight with Brainiac, the Legion experiences relative peace. Cosmic Boy found this suspicious as they hadn't heard from any of their enemies in a long while. Cosmic Boy then went to face a futuristic Joker called the Jester, who was stopped by a new hero called Nightwing and Saturn Girl. Cosmic Boy asked Nightwing to join the Legion as they could use someone like him, but Nightwing refused at first. After eventually agreeing, Cosmic Boy gave Nightwing a belt and a ring. After being showed the Batcave, Cosmic Boy showed Nightwing Legion HQ. Cosmic Boy goes up against the returned Joining's Super Droids and ends up reluctantly going along with Nightwing's plan due to Superman's consent. Cosmic Boy handled the Green Lantern-Droid and tries to crush it with a magnetic field, but the droid defends with green energy before Cosmic Boy stabs it in the chest with a yellow pole. Cosmic Boy then helps Lightning Lad keep the Robin-Droid steady while Bouncing Boy totals that one. He was also against the idea of salvaging the droids.
Lightning Lad/Garth Ranzz - Three years after the fight with Brainiac, the Legion experiences relative peace. Lightning Lad voiced how everything had been pretty quiet. When a futuristic version of the Joker, the Jester, arrived, Lightning Lad witnessed his confrontation with a new hero called Nightwing. Though excited at finally getting a fight, Lightning Lad immediately got confused with Nightwing and Jester's presence. He did offer help but got turned down. After Nightwing turned down a chance to join the Legion, Lightning Lad convinced him by talking about how he could help people. When Lightning Lad learned of Nightwing's lineage, he called it cool. Lightning Lad was taken to the Batcave and wondered at how Batman was able to preserve all the information that was lost after the Great Crisis but was excited by it. On the view screen, Lightning Lad witnessed Brainy getting captured by Alexis Luthor. After Nightwing got blasted with red sunlight energy, Lightning Lad confronted Alexis with Saturn Girl and Shrinking Violet. After Brainy was freed and Alexis disappeared, Lightning Lad invited Brainy back into the Legion. Lightning Lad is present when the Joining begins approaching Earth, and goes off to face them with the others. When they're confronted by rebuilt Super Droids, Lightning Lad's ready to fight. Lightning Lad ends up fighting the Flash-Droid and destroys it by firing right in front of the speeding droid. After that, he holds the Robin-Droid steady while Bouncing Boy finishes that one off. Lightning Lad then notes that used the right way, the droids could be pretty handy. Lightning Lad is then surprised when the fight is over, and the Joining are defeated. Lightning Lad then welcomes Kell back to the team. Lightning Lad later learns that Ayla has been kidnapped and vows to go after Londo. He refuses the aid of the team at first until Nightwing assists that they come. Once they arrive, Garth states that if his sister is hurt, he'll tear Londo to pieces. Once they got to Londo's lab, he blasted Londo back and went to his sister, who had been artificially aged to a teenger. Lightning Lad then assures Ayla that she'll be okay. He was against Ayla helping until she pointed out she had the same powers as him. After Ayla incapacitates the monsters, Lightning Lad agrees with Ayla that he should go to jail until he disappears. Lightning Lad then accepts Ayla into the Legion of Superheroes.
Saturn Girl/Imra Ardeen - Three years after the fight with Brainiac, the Legion experiences relative peace. Saturn Girl distrusted the peace since it got too quiet for her. After an alarm sounded, Saturn Girl met the hero Nightwing and his nemesis, the Jester. When Jester lunged at her, Saturn Girl knocked him out by kicking him into the wall. Once Nightwing joined the Legion, Nightwing showed Saturn Girl the Batcave. On the view screen, Saturn Girl witnessed Brainy getting captured by Alexis Luthor. After Nightwing got blasted with red sunlight energy, Saturn Girl confronted Alexis with Lightning Lad and Shrinking Violet. After Brainy was freed and Alexis is knocked down, Saturn Girl's about to declare that Alexis was going to jail until she disappeared. Saturn Girl helped fight off the returned Joining's Super-Droids and defeated the Martian Manhunter-Droid by telekinetically tearing off its chest piece.
Bouncing Boy/Charles Taine - One day, Bouncing Boy discovers an odd energy signal which turns out to be the Joining. Bouncing Boy is excited to see Superman again when he returns. When the Joining releases Super Droids, Bouncing Boy fights the Robin droid and has trouble with it until Cosmic Boy and Lightning Lad help him out.
Brainiac 5.1 "Brainy" - Three years after leaving the Legion, Brainy was attacked by the Scavengers. Brainy used a force-field installed into his belt and newly discovered laser vision to stop them. Brainy was then captured by Alexis. In a LangCorp building, Brainy tried to reach a release button to free himself, but he couldn't reach it. Brainy's then freed by the help of Lightning Lad, Saturn Girl, Shrinking Violet, and their new ally, Nightwing. Brainy advised Alexis to give up before catching her fist, due to still having the strength he possessed in battle mode. Brainy then knocks Alexis down just as she disappears. When Lightning Lad asked Brainy to rejoin the Legion, Brainy wasn't sure until Shrinking Violet asked him to join as the Legion wasn't fun without him. After that, he agreed. After returning, Brainy received a new super-suit made from the same material as Superman's. When the Joining arrived, Brainy explained what they were and what their intent was. Brainy then recruited Superman to help them. Brainy then identified the Super Droids when they arrived. Brainy then compliments Shrinking Violet's defeat of the Green Arrow-Droid before Brainy blasts the Hawkman-Droid's chest off. When the Joining retreats, Brainy theorizes that it was because they weren't expecting such strong opposition.
Timber Wolf/Brin Londo - When Ayla went missing, Timber Wolf was the first to believe that it was his father. He also states that Lightning Lad will need help fighting. Timber Wolf also encouraged Lightning Lad to calm down. Timber Wolf then confronts his father and demands that Ayla be let go until he unleashes several monsters. Once Londo was KO'd, Timber Wolf agreed that he should go to jail before he disappeared.
Chameleon Boy/Reep Daggle - Three years after the fight with Brainiac, the Legion experiences relative peace. Shortly after asking about any new missions, Chameleon Boy ended up confronting the Jester before the arrival of a new hero named Nightwing. After the defeat of Jester, Chameleon Boy was excited about the fact that Nightwing was real and questioned his S-Shield, learning he was descended from various super-heroes from the golden age of heroes. Chameleon Boy was then shown the Batcave. Chameleon Boy talked about the returned Brainy's new outfit just before the Joining attacked.
Triplicate Girl/Luornu Durgo - Triplicate Girl is at HQ when the Joining arrives. She then inquires what the Joining is.
Shrinking Violet/Salu Digby - On the view screen, Saturn Girl witnessed Brainy getting captured by Alexis Luthor. Shrinking Violet insisted on saving Brainy After Nightwing got blasted with red sunlight energy, Shrinking Violet confronted Alexis with Lightning Lad and Saturn Girl. Shrinking Violet shrank down and entered the control panel that controlled Brainy's restraints. Shrinking Violet then sabotaged it, and Brainy was released. After Alexis disappeared, Shrinking Violet convinced Brainy to return by stating that the Legion wasn't fun without him. Shrinking Violet helps fight the returned Joining's Super-Droids and shrinks down and enters the Green Arrow-Droid before internally damaging it and coming back out, getting praised by Brainy.
Lightning Lass/Ayla Ranzz - While Ayla was playing on the farm of Winath, she was captured by Dr. Londo's monsters and teleported to Rawl. where Dr. Londo planned to experiment on her, while she cried for her brothers. After Ayla's age was accelerated to fifteen, the Legion arrived, and she was rescued by Lightning Lad and the new member, Nightwing. She then decided to help against Londo's monsters, electrocuting them. She then decided that Londo should go to jail before he disappeared. After that, Ayla joined the Legion and took the name Lightning Lass.
Brainiac - Three years after becoming Brainiac 6, Brainiac voiced that it was time to begin his attack. Shortly afterwords, Brainiac had Alexis Luthor, the descendant of Lex Luthor, brought to him. Brainiac then asked Alexis to push Brainy back to the Legion due to requiring Brainy's knowledge of being organic to become complete. Brainiac then promised to do his best to bring Superman back to the future. After Brainy returned to the Legion, he rescued Alexis. Brainiac then began planning on how to bring Superman to the future. Brainiac strikes a deal with the Joining to have them attack Earth to force the Legion to call in Superman for assistance. Brainiac then notes how only one more piece is required before openly acting. After Dr. Londo's actions lead to Ayla becoming the Legionairre, Lightning Lass, Brainiac agreed to his end of the deal for Dr. Londo, and he downloaded all his knowledge into him, resulting in Dr. Londo going into a coma.
Alexis Luthor - Five years after her fight with the Legion of Superheroes, Brainiac approached Alexis about joining forces with him. Alexis then agreed to kidnapping Brainy to indirectly force him back into the Legion as long as Brainiac brought Superman back to the future. Alexis then had the Scavengers attack Brainy and managed to capture and restrain him in a Lang Corp building. Alexis explained that the bonds were too strong for Brainy to struggle out of, which they were. Alexis then claimed this was boring until the new Legionaire, Nightwing, arrived. Guessing his Kryptonian heritage from the Super Shield he wore, Alexis blasted Nightwing with Red Sunlight energy to stop him from saving Brainy. Alexis was then confronted by Lightning Lad, Saturn Girl, and Shrinking Violet. Nightwing then broke free of the Red Sunlight energy by blasting the laser with a star bolt. Once Shrinking Violet saved Brainy, Alexis tried to punch Brainy out, but Brainy caught her fist and easily tossed her down. Alexis was then saved by Brainiac.
Jester - A futuristic version of Joker and an enemy of Nightwing. He went to New Metropolis before being confronted by Nightwing, who kicks him in the jaw as a hello. Jester then attacks with a Kryptonite laser that Nightwing shields himself from before using his mental powers to disintegrate the ray. Having fun, Jester lept at Saturn Girl before she knocked him out.