In order to enlist help against a group of wrongdoers, Brainiac 5, Saturn Girl, and Bouncing Boy travel back to the 21st century to recruit the hero that inspired the foundation of the Legion of Super Heroes ― Superman. However, Brainiac 5 travels back to when Clark was much younger and still developing his powers. Reluctantly, Clark accepts to help the heroes, and accompanies them to the 31st century. There, the young contender must prove his worth, all the while coming to terms with his own destiny.
While on a space mission, the Legion of Super Heroes gets a distress call from a jungle planet. Dr. Londo, the scientist who sent out the SOS signal, asks the heroes to make him safe from a maverick wolf creature that went on a rampage and killed his son. During their quest, the Legionnaires ascertain that this ordeal holds more than meets the eye.
Clark saves the life of Alexis, a powerful and wealthy individual, who soon becomes close friends with him, but Superman's responsibilities to the Legion forces Alexis to resort to means of keeping Clark to herself.
Superman opens a Pandora's box in the form of a Phantom dimension, unleashing an opponent with powers that match his own and threatening the Legion with eternal entrapment within the confines of the dimension
Lighting Lad's competition in the Galactic Games forces him to go head to head with someone close to him. Superman and Phantom Girl uncover a conspiracy within the games to sabotage the event
The team shelter from a storm within the confines of a long abandoned space station, only to vanish one by one, confronted and tortured with their deepest fears
Superman, Timber Wolf, and a disembodied Brainiac 5 travel to uninhabitable regions of the galaxy searching for a way of saving Brainiac's life
Lightning Lad abandons his teammates and joins an older, more refined group of heroes, but there is more to them than one could realize...
A group of failed Legion qualifiers unite to save the world any way they can when the Legion itself becomes preoccupied with a threat from above
A mischievous Sorcerer reeks havoc on Earth, Superman discovers another dangerous counter to his formidable powers...
Lightning Lad travels with the Legion to his troubled home world of Winath, a trip that reunites the team with their long-absent leader Cosmic Boy, and he is not alone...
The Legion faces the might of the terrifying Sun-Eater
With the Sun-Eater poised to consume Earth's sun, the Legion and their most vicious enemies unite to halt its progress, but one must die so that Earth can live.
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.