Issue 1 begins with the Time Trapper plotting from the end of time to rid the universe of the Legion of Super-Heroes and, to start the ball rolling, hurls Superboy-Prime towards the era of the Legion. Arriving in a similar fashion to Superman’s arrival on Earth, it isn’t long before Prime realises when he is. In the Smallville of 3009, Prime enters the Superman Museum and receives a tour guided by a holographic Jimmy Olsen. The hologram gives Prime a quick run through Superman’s history before arriving at the Legion who were inspired by Superman before discovering the Hall of Villains where, among the villains who troubled Superman throughout his career, Prime is horrified to discover he himself is little more than a footnote. Enraged by being almost completely forgotten, Prime destroys much of the museum and swears to ruin everything Superman inspired before being informed by Olsen of the Legion of Super-Villains.
Elsewhere, the leaders of the Legion are confronted by the leaders of the United Planets Council who are planning to disband the Legion, claiming that humanity has revealed itself to be inherently xenophobic against alien races. While that’s going on, other members of the Legion brave the Phantom Zone to rescue Mon-El/Lar Gand. At the Council, when things appear to be going wrong, R. J. Brande, the man responsible for creating the Legion, arrives in order to help his young friends.
With information from the Superman Museum, Prime flies to the prison planet Takron-Galtos and frees long-time Legion enemies and the leaders of the Legion of Super-Villains, Lightning Lord, Saturn Queen and Cosmic King. When they are all together, the villains reveal to Prime that, as Superman inspired the Legion of Super-Heroes, so Prime had been the inspiration for the Villains.
At the Council, as R. J. Brande begins to sway the members away from disbanding the Legion, he is shot by an old rival; his death reveals Brande to have been an alien shape-shifter and his killer a xenophobic human which fuels the Council in their decision against the Legion. Brande’s killer is quickly killed by the Time Trapper who operates in secrecy. The Legion later convene to try and decide what to do only to receive an image from Takron-Galtos that makes them summon Superman from the 20th century – a flaming S-shield burnt into the planet’s surface and every prisoner freed. Determining to fight Prime, a Superboy from a parallel universe, Superman and the Legion decide to recruit two other Legions from parallel worlds in order to help redeem Prime.
Issue 2 starts with Shikari, one of the Legion Lost characters, confident of finding a way out of the Limbo she and the others are in.
On the Sorcerer’s World, an imprisoned White Witch is plagued by visions before the Time Trapper stops them to prevent her seeing his plans. She is saved a moment later by several members of the Legion who rescue her from her cell. As they attempt to rejoin their backup, Green Lantern, they find that he is under attack by the Legion’s old foe, Mordru. Though they try their best to defeat him, they are stunned by the arrival of Superboy-Prime and many of the villains he had released from the prison planet Takron-Galtos.
On Earth, Superman and the Legion argue over the best way to deal with Superboy-Prime and briefly flirt with the idea of killing him before Cosmic Boy emphatically refuses to do it.
Green Lantern shields the other Legion members giving White Witch enough time to summon a portal to Earth which he forces the through. With them gone, his shield is destroyed and he faces Superboy-Prime.
As the Legion continue to argue, the White Witch and her rescuers arrive at Legion HQ and, after telling them what happened to Green Lantern, try to open another portal back to Sorcerer’s World to save him. The Lantern, meanwhile, suffers a severe beating from the villains and is killed by Superboy-Prime as White Witch, still weak from her capture, is unable to open a portal. Upon his death, Lantern’s ring flees the sector as Mordru is persuaded to join the Legion of Super-Villains.
Brainiac comes up with a plan and splits the Legion into teams; some, including Brainiac, travel to the Justice League’s original headquarters to find the crystal ball the League first used to contact the Justice Society years before; others make a trip through time to the 21st Century; others take Green Lantern’s body from Sorcerer’s World to Oa; while Superman and the strongest of the Legion face off against Superboy-Prime and his Super-Villains who have travelled to Earth. Brainiac’s plan works and the Legions of two other worlds, including those lost in Limbo, are brought to the League’s headquarters.
Arriving on Oa, Mon-El and Shadow Lass present the body of Green Lantern to the last of the Guardians of the Universe, Sodam Yat.
Issue 3 begins with Sodam Yat cremating the last of the Green Lanterns and initially refusing Mon-El and Shadow Lass’s request to restart the Green Lantern Corps. They do, however, convince Yat to join them in their battle against Superboy-Prime, ending years of inactivity on Yat’s part.
On Earth, in Metropolis, the Legions of Super-Heroes and Super-Villains battle against one another before Superman appears and tackles Prime head on. Superman attempts to reason with him, prompting him to remember his original home of Earth-Prime and his family but the tactic fails and simply enrages him. Meanwhile, the xenophobic Earth-Man and his Justice League have attacked the United Planet and despite a spirited defence, there are casualties on both sides. Above the city, Mordru unleashes dozens of Shadow Demons in an attempt to find the White Witch, killing innocents as Prime rejoins the battle. He is matched, though, by the return of Superman who has brought the members of the three different Legions with him. With the help of the new Legions, the tide of the battle begins to turn as the Legion of Super-Villains suffers one defeat after another. The Brainiacs of the the Legions recruit all the lightning wielders the Legions hold to carry out the second part of their plan.
Back in time, in the 20th century, three of the Legionnaires have travelled back in time to Smallville where they find the young Lex Luthor. With Luthor in his makeshift lab, the Legionnaires sneak in to his bedroom and steal one of his hairs from his pillow.
In the future, the three Brainiacs have brought together the Legionnaires they need. They explain to Xs that she is not from Earth-247 which, as shown in Infinite Crisis, was recently destroyed. The Brainiacs altered Starman’s uniform, transforming it into a map of the multiverse, which allowed him to return the Legions to their respective homes, though they lost all memory of the events. With Xs back on her home planet, she has to run to help the Flash family that she is a part of.
In the battle against Prime, as the Legionnaires strip him of his armour, Saturn Queen warns him of the Brainiac’s plan. Fearing the results, Prime tries to head off to stop them but is attacked by Sodam Yat as a strange form of lightning lights the skies. The Fatal Five attack the Legion headquarters where, at Brainiac’s command, Xs uses a cosmic treadmill to reach lightspeed at which point the lightning wielders strike her, opening up a gateway to the Speed Force. Desperate to prevent the success of the experiment, Prime attacks just as it works and Bart Allen, Kid Flash, is restored to life.
Issue 4 begins in the present, with Starman working as a grave digger in Metropolis, digging up the grave of a “Mr. Kent.”
In the 31st century, the Legionnaires find Mordru at the centre of the Shadow Demons and attack him using their own mystics and Superman. In the midst of the battle, they are distracted by the lightning at Legion headquarters that heralds the return of Kid Flash and his ongoing battle with Superboy-Prime. He and the Legionnaires attack Prime, allowing Brainiac to continue with his plan – in the Arctic.
As Sodam Yat joins the battle against Prime, Superman discovers Kid Flash’s return and again tries to reason with Prime before he and several of the Legion are literally snatched away by the Time Trapper. At the end of Time, the Trapper admits he was behind Prime’s appearance in the future and that he wants to destroy the Legion and Superman.
Having refused to join the fight from the start, news reports of the Legion’s casualties fire up Sun Boy while outside, one of the Legion’s Element Lads changes the rubble around Prime to Kryptonite. As it has never affected him before, he is surprised when it hurts him and he is saved only by Cosmic King converting it to yellow sunlight, quickly repowering him. Mordru suddenly warns Prime and the Legion of Super-Villains leaders that they need to destroy Superman’s Fortress of Solitude to prevent whatever Brainiac is planning from coming to fruition. As they flee North, some of the Legion follow them.
At the Fortress, the Brainiacs are joined by their time travelling friends fresh from Lex Luthor’s bedroom with a sample of his hair. In the depths of the fortress, they find something that Starman had buried a thousand years before and raise it: the Kryptonian chrysalis that had helped restore Superman’s body following his death at the hands of Doomsday. As the Legion try to stop Prime reaching the Fortress, the Brainiacs use Luthor’s hair to infuse the chrysalis with his DNA but before they can complete the process, Prime’s attack causes a cave-in. As the Brainiacs are knocked unconscious, Dawnstar and Wildfire are left to try to finish the plan as Polar Boy tries to delay Prime. Despite having been a substitute Legionnaire, Polar Boy bravely faces Prime down long enough for Sun Boy to arrive and attack Prime while Dawnstar and Wildfire complete the plan started by Brainiac.
As Prime counter attacks, Conner Kent, Superboy, is reborn and attacks.
At the end of time, Superman and the Legion’s founding members see his return and launch their own attack against the Time Trapper as Superboy attacks Prime, only to reveal to everyone that Prime and the Trapper are one and the same person.
Issue 5 begins at the end of time with the Time Trapper explaining how his journey through the multiverse had changed him into an anomaly.
In the 31st century, Superboy, the Legion, Kid Flash and Sodam Yat all attack Prime.
Saturn Girl, at the end of time, uses tears in reality to contact Brainiac in the 31st century and revealing the Trapper to be Prime. In Metropolis, Mordru drains the Legions of their powers and recharges the Super-Villains, leading the White Witch to realise a sacrifice needs to be made by her.
As Superboy attacks Prime, he burns him with his heat vision, marring the S shield Prime had carved into his own chest. At the end of time, Saturn Girl see the same wound appear on the Trapper’s chest proving that the destiny the Trapper had seen was not certain – things could be changed. Brainiac uses the knowledge to devise a plan and asks Saturn Girl to weaken the Trapper as much as possible. As Superman battle the Trapper, Saturn Girl sends out a telepathic distress call to multiple parallel worlds and the various Legions respond with dozens of alternate Legionnaires coming to her aid.
In Metropolis, the White Witch attacks Mordru, using his own spells against him, forcing a type of merging to take place, creating the Black Witch. With her increased power and returning Legionnaires, the tide of battle turns in the Legion’s favour.
At the end of time, the cobined Legions manage to knock the Trapper unconscious and Brainiac tells them to bring him to the 31st century and the battle with Prime. There the Trapper meets Prime who is not convinced they are the same person and hits him. Before the assembled Legionnaires, both Prime and the Trapper vanish.
As things calm down, Superman greets Superboy again and the Brainiacs speculate that Prime may never become the Time Trapper; that it, like the defeat of the Legion the Trapper saw, was simply one of a multitude of futures.
Unknown to them, on Earth-Prime itself, Prime returns to his home but his joy is short lived as his parents reveal they have been reading all of the stories we have read, revealing Prime’s instability and his murderous actions.
In the 31st century, the Legions count the cost of the battle, honouring their dead and welcoming new members while the Black Witch returns to rule Sorceror’s World. The three Legions use cosmic treadmills to open portals to their own worlds, returning them to the proper times and places.
In the present, Superman reveals the returned Superboy and Kid Flash to the Teen Titans.
On Earth-Prime, Superboy-Prime has cowed his parents into serving him while he plots revenge.