Action Comics #864 is the Epilogue to this story. Lightning Lad and Superman catch up on old times when Batman interrupts them. They find the bodies of Karate Kid and Una in Gotham after their deaths in Countdown. This story is proceeded by The Lightning Saga and succeeded by Final Crisis: Legion of Three Worlds.
Detailed Plot Summary
Chapter One: Alien World
The story begins in 3008 AD on an unidentified alien world. The planet is consumed in civil war and its people are nearing mutually-assured destruction. An alien couple decide to send their child to Earth, in the example of Superman. The father states that more than a thousand years ago (the present day), Kal-El was sent to Earth and became the universe's greatest hero, the ultimate symbol of truth and justice. The alien parents believe that Earth is the only hope for their son and send him off in a spaceship as their planet explodes into destruction. As the spaceship with the baby inside speeds into Earth's atmosphere, it passes by the Human Cultural Center satellite before crash-landing in Smallville. An old couple passing by in their truck witness the landing of the craft, and approach it to investigate. As the alien child crawls out from the spaceship, the wife asks the husband what they should do. The husband replies that they should do what all law-abiding citizens would, and pulls out a shotgun.
In the present day, at the Daily Planet, Clark Kent rushes towards the elevator but the people inside ignore him and don't bother to keep the door open for him. He has a brief chat with Jimmy Olsen before Perry appears and begins lecturing Clark. He states that Clark has a problem, citing Clark's lack of friends aside from Olsen, and tells Clark that he's a hell of a reporter but that he needs to learn how to reach out to people. As Perry continues chiding Clark for his lack of self-confidence, Clark hears cries of panic and uses his X-ray vision to look through the walls of the Daily Planet. He sees the source of the panic - a giant Brainiac trampling through the park. Clark quickly excuses himself, jumps out of window and changes into Superman. After some quick punches, Superman tears off the robot's face, only to reveal a monitor inside it. A mysterious green-skinned man tells Superman that his future needs him. A rainbow-colored ray shoots out of the monitor and hits Superman as the story flashes back to Clark's past.
We then go back to Clark's time as a teenager, as he stares sadly at the popular crowd - a group of football stars and pretty girls. He overhears them talking about him, and they comment on how he always acts as though he's afraid of getting hurt and of how creepy he is. As Clark walks off alone, he suddenly sees a passing bird flying beside him, and quickly looks around. After making certain that there's no one around, he leaps into the skies and flies with a flock of birds. After a while, he lands, only to find himself face-to-face with three flying teens. They introduce themselves as Cosmic Boy, Saturn Girl, and Lightning Lad, and they tell him that they wanted to meet and thank him. Clark is surprised when they tell him that sometime soon the world will accept him, and Cosmic Boy gives him a Legion flight ring. As they fly off, heading towards their time sphere, Clark asks if he can follow them to the future. Lightning Lad persuades Cosmic Boy to let him, and Clark goes to the future - where he meets the Legion of Super-Heroes.
Back in the present, the ray has made Clark remember his school-day adventures with the Legion, and he recognizes Brainiac 5 as the man in the monitor. Brainiac 5 then goes on to say that the Legion chose not to involve Superman in the future crisis but that they now have no choice but to. The Brainiac robot's chest cavity opens up, revealing a time sphere inside, and Brainiac tells him to step inside to go to the year 3008. A flight ring is inside the time sphere, and the sphere vanishes as it sends Superman hurtling into the future.
When Superman finally arrives, he stumbles out of the time sphere into the Legion's headquarters, only to find it in shambles. The statue of Superman and the Legion has been broken and defaced, and when Superman turns around, he sees members of the Science Police training guns on him. Just before they shoot him, Colossal Boy suddenly emerges from the walls and knocks out all of the officers with one blow. Shrinking back down to normal size, he collects the Legion flight rings before recognizing Superman. Dawnstar and Wildfire also appear and when Superman explains how Brainiac 5 contacted him, Dawnstar replies that Brainiac 5 has been missing for over six months. Wildfire then tries to drag Superman back into the time sphere but the sphere is destroyed by Science Police reinforcements. As the SP officers open-fire at Superman and the Legionnaires, Superman holds a hand up to stop them, only to find that the Science Police lasers shoot right through his hand. As Superman stares at his wound in shock, Dawnstar tells him to activate his ring as they all make an escape.
The issue ends with the four of them flying off, as Dawnstar reveals that the Earth's sun has turned red in the future.
Chapter Two: Illegal Aliens
The next issue begins with Cosmic Boy, Saturn Girl, and Lightning Lad zipping down into the Batcave. Batman's headquarters is in a state of ruin in 3008 AD. Cosmic Boy then states that they have to look for proof that Krypton existed, and tries searching for a Kryptonite ring that Batman kept as a safeguard against Superman. He and Lightning Lad have a short spat where Lightning Lad tells him that they should fight the Justice League. Cosmic Boy retorts that it will accomplish nothing, and asks how the Legion would look to Earth's people if they took down their heroes. Lightning Lad replies that he doesn't care anymore, but Saturn Girl interrupts, asking him what would Superman think. Lightning Lad finally concedes at this, and Saturn Girl says that the universe will go to war if they fail - all in the name of Superman. Suddenly, the Justice League of Earth emerges from a hole in the ceiling. Earth-Man, Spider-Girl, Tusker, Golden Boy, Storm Boy and Radiation Roy appear, ready for a fight.
Cosmic Boy uses his magnetic powers to hurl Batarangs and a Batmobile at Earth-Man but Earth Man easily deflects them. Earth-Man asks Cosmic Boy why the Legion refuses to leave Earth, asking him why he doesn't leave like so many other Legionnaires have, and Cosmic Boy replies that the Legionnaires who left Earth did so because their homeworlds exploded into the violence caused by the League's crusade. Tusker throws a punch at Lightning Lad, who dodges it and returns fire with a lightning bolt. But Golden Boy manages to land a punch on Lightning Lad, and Storm Boy finishes him off with a quick lightning strike. Saturn Girl tries to gain telepathic control of both Storm Boy and Golden Boy, but Spider-Girl ambushes her from behind, snaring Saturn Girl in her hair, and throws her off to Radiation Roy. Radiation Roy seizes her, his perverted thoughts causes Saturn Girl to panic, and he shocks her with a quick blast of energy. With Lightning Lad and Saturn Girl down, the Justice League of Earth surrounds Cosmic Boy.
At the former Braal Embassy, Superman has his wound treated by Dawnstar while Colossal Boy and Wildfire start a small fire. Superman asks what's going on and asks why the Legion doesn't want his help, and Dawnstar replies that they were afraid he would be hurt in the red sun (which he doesn't have powers under). Wildfire then states that the Legion agreed that no matter what happened, they couldn't risk Superman's life, as he was the most important figure in intergalactic history. Dawnstar then states that if Superman was killed in the future, everything that he represented wouldn't come to pass - universal laws, the United Planets, peace on Earth, and even the Legion. Colossal Boy then states that Earth is seceding from the United Planets, and begins to bemoan at the loss of his wife - Yera - who was cast out because she was a Durlan. Dawnstar consoles him and tells them that they will find Yera and all the other Legionnaires. Wildfire then says that sending Superman back is a bigger priority, but Superman knows them well enough to realize that they're hiding something from him.
In the Human Cultural Center orbiting Earth, which is the HQ of the Justice League, we learn what that 'something' is. In a classroom inside the center, Eyeful Ethel teaches a group of human schoolchildren about the 'truth' regarding Superman's origins - that he was not an alien, but rather, a human given powers by Mother Earth. She then goes on to say that the humans had been fooled by the Legion, which was secretly an 'alien invasion', and states that many tryouts were rejected by the Legion simply because they were human. She then goes on to say that the focus of today's lesson will be Kirt Niedrigh, formerly known as Absorbancy Boy, who was also rejected by the Legion for being human. She relates how Niedrigh found an ancient crystal that documented the true history of Superman - that he was a human who despised aliens - and talks about how Absorbancy Boy eventually became Earth-Man and formed the Justice League of Earth. As she is talking, one of the kids suddenly gets excited when he spies the Justice League walking past the classroom. The kids begin cheering 'Long Live Humans' as the Justice League carries the bodies of the three Legion founders, encased in triangular cases.
In another room, Earth-Man places the three founders among a collection of captured Legionnaires and absorbs all of their powers (Invisible Kid, Phantom Girl, Ultra-Boy, Shrinking Violet, and Blok are also among those captured). He then gets a call from Spider-Girl, who tells him that a Superman lookalike was reported being seen at Legion HQ and that the remnants of a time sphere were found nearby.
Somewhere else, we see Superman coming to terms with the lies that have been told about him. Superman then states that they have to find Brainiac 5, as he must have had a reason and plan for bringing Superman to the future, and Dawnstar tells him that his trail leads to Alien Holding Camp 6736. She states that there is where her tracking powers tell her Brainiac 5 is, and mentions that she can also sense another Legionnaire inside.
Chapter Three: Lightning and Shadows
In the former headquarters of the Legion, the Justice League of Earth are examining the remnants of the time sphere. Golden Boy states that Earth-Man said Superman would never returned, and Earth-Man replies that they have to keep the truth about Superman from spreading. Spider-Girl comments that Superman is powerless under the red sun, and Earth-Man says that this is their chance to end it. Once Superman is dead, his name and story will belong to the Justice League of Earth - forever.
In Alien Holding Camp 6736, a Legionnaire is being beaten up by the camp's warden. The Legionnaire refuses to tell the warden what he wants to know, and the warden continues turning up the heat as he resumes punching the Legionnaire. Suddenly, one of the camp's guards contacts the warden and tells him that the camp is under attack by the Legion. Colossal Boy, Wildfire, Dawnstar, and Superman break into the camp and begin freeing the aliens imprisoned there. Superman beats up a number of the guards, sustaining a wound on his forehead, and notices the freed aliens staring at him with skepticism. Superman says that he is who he says he is, but a Korugarian child comments that Superman doesn't bleed. Dawnstar leads them to Brainiac 5's cell, but there's no one inside, and Dawnstar senses that Brainiac 5 had somehow managed to teleport himself back to Colu. The four of them then make contact with the second Legionnaire who was captured there - Polar Boy. Polar Boy has lost his right arm, but makes an icy copy with his powers, and tells Superman that Brainiac has a plan to convince Earth about Superman's true heritage. He then states that him and Brainiac 5 were on their way underground before being captured by the Justice League.
Suddenly, darkness envelopes the four of them, and Shadow Lass and Night Girl appear. Shadow Lass teleports the four of them and the freed aliens to their 'clubhouse' - a secret location which the Legion uses to help aliens flee back to outer space via wormholes. There, they meet Lightning Lass and Timber Wolf, and Timber Wolf gives the rundown on what happened to all the other Legionnaires (Mon-El was banished to the Phantom Zone, Spider-Girl traded White Witch to Mordru in exchange for Earth's safety, Chameleon Boy returned home to Durla et cetera). Lightning Lass begins programming one craft for Colu, before they all hear Earth-Man in their heads. The Justice League of Earth suddenly ambush the clubhouse - revealing that they were following them through Earth-Man (who was using the telepathy he stole from Saturn Girl).
Earth-Man blasts Shadow Lass with a lightning bolt he stole from Lightning Lad, while Night Girl begins punching Radiation Roy. Lightning Lass attacks Spider-Girl, and Dawnstar and Timber Wolf try to prevent Superman from interfering with the fight. Timber Wolf then tells Superman, Dawnstar, Colossal Boy, Polar Boy, and Wildfire that they need to leave for Colu and find Brainiac, and as the other Legionnaires hold the Justice League off, the five of them leave via a wormhole. But just as they flee, Storm Boy manages to fire off one lightning bolt that damages their craft. As they emerge in Colu, their damaged ship is unable to make a safe landing and crash-lands on the planet. When Superman pulls himself out of the ship, he is suddenly surrounded by Coluans who inject wires into him. He blacks out.
Superman wakes up to find himself imprisoned, and comes face-to-face with the new ruler of Colu - Brainiac 5. Brainiac 5 tells Superman that he is to be terminated.
Chapter Four: Chameleons
In Braal, two soldiers are talking as one comments that Earth has seceded from the United Planets. In the background, we can see the Braal army preparing for war with their tanks. On Titan, a group of men and women are discussing about how humans dare question Superman's Kryptonian heritage and their lies about Superman being a xenophobic human. On Winath, as pilots begin readying their planes, a Winath pilot states that Earth's government has begun imprisoning any alien left on the planet. The pilot states that as soon as Colu delivers their strike plans, the United Planets will go to war with Earth.
Back on Colu, Superman is shocked by Brainiac 5's new personality, and Superman thinks that Brainiac 5 has been brainwashed by the Coluans. Brainiac 5 replies that that is impossible, and states that there is no other option but war now - and that humans are emotionally volatile and stupid animals. He then goes on to say that the logical choice would be to eliminate Earth, and he then tells his robotic guards to continue the strike plan calculations. Brainiac 5 says that he will kill his former colleagues himself, and the robots leave him to it. But when the robots are gone, Brainiac 5 finally reveals his ruse and asks Superman with a relieved, "What the hell took you guys so long?". As the other Legionnaires wake up, Brainiac 5 releases them from their imprisonment and explains what he's been doing all along. He states that he set himself up as Colu's ruler to slow down their strike plans against Earth. He then states that he has also planted a spy inside the Justice League's headquarters.
In the Human Cultural Center, the children there are with the Justice League as they observe the newly-captured Legionnaires in their cases - Shadow Lass, Lightning Lass, Night Girl, and Timber Wolf. As the kids eventually leave for their bus, Earth-Man states that it is time for the next stage of their crusade: to locate and execute every alien on Earth. He states that they will head for Earth in two hours. As the Justice League go off-duty, a lawyer visits Golden Boy and asks him to pay for his mother, who wants a vacation to a Paris spa. Golden Boy seems annoyed by this, and states that he never received anything from his mother except lawyers begging him for money. He then touches the lawyer, turning him into a statue of gold, and tells his servants to give that to his mother before saying that he wants to be polished. Meanwhile, Storm Boy is angry that he failed to stop Superman and the other escaping Legionnaires, and tells his surgeons that he wants to increase his power capacity. The surgeons tell him that they need to remove his heart for the procedure, and that they can't use anesthetic, but Storm Boy tells them to do it anyway. Elsewhere, Spider-Girl and Radiation Roy are reminiscing about their days in the Legion of Super-Villains before Roy tries to cop a feel. Roy opens up his helmet, revealing his hideous, tumor-covered face, and asks Spider-Girl 'just once...for old time's sake'. Spider-Girl replies, 'Not with that face'. In Earth-Man's room of captured Legionnaires, he absorbs all of their powers and puts on a red cape with an Earth logo on it.
As he walks off, a little girl emerges from the walls and finds Legionnaire Sun Boy hooked up to a machine that's feeding off of his powers. The little girl begins recording a log, stating that Brainiac was right and that Sun Boy has been imprisoned and used to turn the sun red - before she is choked by an invisible hand. Earth-Man suddenly emerges, stating that he had heard the girl's thoughts earlier, as the girl transforms to her true form - Chameleon Girl. Back on Colu, Colossal Boy slams Brainiac 5 to the wall when he learns that Yera is Braniac's spy. They have a brief verbal spat before Superman calms everyone down, stating that he trusts Brainiac. Brainiac then tells Colossal Boy that he wouldn't have sent Yera in there if she couldn't handle herself. Colossal Boy finally softens, and hands Braniac 5 a Legion ring. Suddenly, the Coluans emerge and try to arrest Brainiac 5 - stating that he is a traitor to the United Planets. Braniac 5. Earth-Man had earlier read Timber Wolf's mind, learning that Brainiac 5 was simply conning Colu, and was the one who tipped off the Coluans.
As the Coluans attack, the team flee in another spacecraft. As they fly away from Colu, Brainiac 5 states that without him slowing them down, the Coluans will finish formulating the United Planets strike plans in another four hours.
Chapter Five: Revenge of the Rejects
The issue begins with a flashback to both Superman and Polar Boy's earlier days. We see Clark failing at baseball and then meeting the Legion. We also see Polar Boy failing to control his powers and then meeting the Legion of Substitute-Heroes. In Superman's narration, he states that he knows what it feels like to be rejected, but that it doesn't mean you get a free pass to take it out on the world. He also says that you can't shut yourself off from others, or you might miss people that you'll fit right in with.
Back in the present day, in the spacecraft with Brainiac 5, Dawnstar, Colossal Boy, Wildfire, and Polar Boy, Superman states that they should call in the Substitute-Heroes. Wildfire questions their reliability - as they're also rejects like the League - but Brainiac 5 explains that the League's members were rejected because their telepathic profiles revealed psychotic tendencies and deviant obsessions. Brainiac 5 then reveals that he has been in communication with the Subs since they went underground, and they agree on sending them in. At the Human Cultural Center, Earth-Man continues to fight with Yera, before defeating her. As he knocks her out, he begins screaming about how Superman should have been rejected and that he was the real pretender. In the classroom, Ethel is talking to Tusker and comments on how late the school bus is. She suddenly spots the bus approaching towards a window, and is pushed aside by Tusker just as the bus crashes through into the satellite. The bus slams through multiple rooms, interrupting Golden Boy's polishing, Storm Boy's operation, and even Radiation Roy with Spider-Girl. As the bus slams to a stop, Stone Boy bursts out of the vehicle and hits Radiation Roy.
The Substitute-Heroes emerge from the bus' wreckage, all triumphant and ready to fight. Among its members are Rainbow Girl, Chlorophyll Kid, Stone Boy, and Fire Lad. Ethel tries to get them to renounce their Legion membership and join the League, but Rainbow Girl quickly turns on her red 'rage' power and attacks Ethel. Chlorophyll Kid throws roses at Storm Boy, while Fire Lad uses his flaming breath to melt Golden Boy. Radiation Roy and Spider-Girl attempt to break Stone Boy, while Rainbow Girl seizes hold of the school bus with her blue 'hope' powers and crushes Tusker with them. In other part of the Center, Superman and the team break in while the Subs distract the League and split up. Polar Boy, Wildfire, and Dawnstar are sent to aid the Subs, while Superman, Brainiac 5, and Colossal Boy head off to rescue the other Legionnaires.
Superman's team finds the other captured Legionnaires, encased in their triangular cages. Brainiac 5 notices the crystal tablet that tells of Superman's 'true human heritage' nearby (the one that Earth-Man found), and comments that it appears to be a real relic, and not fabricated. Finally, the three of them locate Sun Boy, and realize that the Justice League was using his powers to turn the sun red. As Brainiac tries shutting the device down, Yera suddenly emerges and falls into Colossal Boy's arms. While Colossal Boy asks his wife if she's alright, Superman notices a draped glass case in the corner and pulls it off to reveal the real Yera inside it. The 'Yera' in Colossal Boy's arms absorbs his powers before transforming back into Earth-Man. After knocking Colossal Boy out, Earth-Man and Superman break out into a brawl. Earth-Man beats Superman mercilessly, before Superman slams Earth-Man out a window and into space.
Chapter Six: Sun Rise
As the forces of the United Planets approach Earth, Superman and Earth-Man continue fighting in space. Earth-Man flies Superman down to the planet's atmosphere with the intent of crushing him all over the ground. In the Cultural Center, Colossal Boy frees his wife while Brainiac 5 frees Sun Boy. But the Sun is still red, and Brainiac 5 explains that the connection will only be cut when Sun Boy is conscious. He then tells Yera that she needs to kiss him (citing Sun-Boy's attraction to brunette girls), and she does so by transforming to a brunette (albeit reluctantly). With Chameleon Girl's kiss, Sun Boy wakes up and the Sun is restored to yellow just as Earth-Man hurls Superman towards the planet. As Superman falls to the ground, the Sun returns to its original form, and Superman regains his powers. As he lands on the streets, he tears open a Science Police van and frees the aliens that were being locked inside. A Science Police officer tries to shoot him, but he deflects the beam with his hand, saying that he fights for the rights of everyone - human and alien.
Earth-Man suddenly emerges and throws a lightning bolt at Superman. Superman tells the Science Police officers to get everyone clear, and tells them to be 'nice to each other while he's gone'. He then breaks into a brawl with Earth-Man. Earth-Man attacks Superman with Phantom Girl's phasing, Lightning Lad's electricity, and Blok's strength, and asks Superman 'what do you have to beat me'. Superman replies, 'the real thing', just as the entire freed Legion appears behind him, ready to fight. The Legion members all attack Earth-Man, but he is able to repel all of them with the multiple powers he has. As he realizes that his ruse is breaking down and that his entire plan is falling apart, Earth-Man charges at Superman, screaming that Kal-El was never an outsider. Superman knocks him out with one punch and says, 'I've been an outsider all my life'. Lightning Lad congratulates Superman on his knockout, but Brainiac 5 notes that he's picking up Coluan transmissions.
In outer space, as the United Planets approaches Earth, a Braal officer spots Superman and the Legion forming a line in Earth's atmosphere. Superman tells the United Planets to go home, and that there won't be any war today.
24 hours later, the Legion regroups in their old headquarters with Superman, and Cosmic Boy comments on how much work they have ahead of them. He states that the United Planets aren't happy with either the Legion or Earth. Brainiac 5 states that the Justice League are on their way to Takron-Galtos and that the Subs have taken over the Human Cultural Center. The Legion then say that they're going to find all of their lost members, and Superman tells them that no matter how dangerous it is, he wants them to call him the next time they need his help. Brainiac 5 replies that they will, and then they send Superman back to his own era.
The story ends with Superman returning to the spot where he used to meet the Legion after school, back in his younger days. A L was carved into the nearby tree by Lightning Lad, and it's still there after all these years.