Kell-El, the cloned Superman X from the 41st century, comes back to the Legion's time in the 31st century to ask for their assistance against Imperiex, who has devastated the Earth of his time.
Loose in the 31st century, Imperiex frees the Legion's greatest foes from prison to act as his new army. Outgunned and outmanned, the Legion must once more bring Superman from the 21st century to help them.
When Timber Wolf is framed for an attack on his father, Chameleon Boy and Phantom Girl try to clear his name... while the rest of the Legion hunt down their rogue comrade.
Lightning Lad's brother Mekt forms an alliance with Imperiex to create a galaxy-dominating tachyon cannon, while Lightning Lad is haunted by the spirit of his dead sister Ayla.
Disappointed in the lack of competent Legion tryouts, Superman seeks out a new member: Karate Kid, aka Val Armorr. However, the other Legionnaires are concerned that Karate Kid has no super-powered abilities, and may prove more of a liability than an asset as they battle Grimbor the Chainsman.
Chameleon Boy's new assignment: infiltrate Imperiex's forces disguised as the Punisher. Unfortunately, things don't go as planned.
An intergalactic bounty hunter from the future sets his sights on a small boy in the 31st century. The Legion move to protect the boy but find themselves with an unexpected ally.
On a mission to the Bottle City of Kandor, Superman learns the truth behind the destruction of his homeworld of Krypton in the 20th century... and which ancestor of a Legionnaire was responsible.
The Legion go on a mission to rescue R.J. Brande, who was instrumental in the founding of the team.
The Legion come to the aid of the Sorcerer's Planet of Zarok, where the magician Mordru has returned to drain the High Council of its power. Unfortunately, the Legion's only ally is their one-time enemy, the impish Zyx.
The Legion battle the Dark Circle with the aid of Dream Girl, who can predict the future. However, the Dark Circle discovers the Legion's secret weapon and turn her against them.
The original Brainiac attempts to corrupt Brainiac 5, with the aid of Imperiex. However, when Brainiac 5 finally chooses sides, there may be no winners.
The Legion engages the new Brainiac 6 in final battle before it digitalizes the entire universe.