The Legionnaires fly to the Arctic and thousand-year-old Superman's Fortress of Solitude. They've gotten word that Imperiex has launched an attack on the Fortress and arrive to find him, Validus, and an army of destructo-bots waiting for them. Superman flies into the Fortress after Imperiex and Validus while the other Legionnaires take on the destructo-bots. He arrives inside only to find them gone, and finds a city in a bottle. Superman disappears in a flash of light… and finds himself miniaturized inside of the city.
The other Legionnaires get inside and a thousand-year-old Superman robot greets them. It explains to them that Superman, Imperiex, and Validus have all been shrunken and teleported into the city, which is Kandor, last surviving outpost of Krypton. Meanwhile, Superman meets with the Kandorians who wonder where he has been for a thousand years. Imperiex is interrogating natives to find "the Messenger" and Superman attacks him, only to discover that the city lies beneath a red sun… which strips him of his powers.
The robot explains that Superman went into Kandor before he could get a power suit to protect himself from the red sun. The Legionnaires take it and miniaturize, except for Shrinking Violet who goes in on her own. The Legionnaires then teleport into the city, and Shrinking Violet discovers that she can't shrink any further, and in fact is several proportionate feet taller than her comrades.
They find Superman and give him the suit, and Brainiac 5 explains that the Messenger is a device that Jor-El, father of Superman, used to stabilize Krypton using synthetic crystal growth. It was kept in Kandor but when "the Terror" came and miniaturized Kandor and stole it, Krypton was destroyed. Imperiex plans to get the Messenger to use against any planet that opposes him, rendering them into sterile globes. When Superman wonders who the Terror was, Brainiac 5 claims that the records were lost.
Once Superman is powered back up, the Legionnaires go after Validus, who is interrogating the city's Chancellor. The Chancellor refuses to reveal the Messenger's location but once the Legionnaires attack, he tries to get to a map. Imperiex takes it from him and flies off with Validus, bringing down the ceiling as a diversion. Brainiac 5 saves the Kandorians, but they draw back in fear and say he looks like the Terror. The Legionnaires go outside to regroup and Brainiac 5 explains that the original Terror was Brainiac 1.0, a super-villain in the 20th century who fought Superman. Worse, he was Brainiac 5's distant ancestor. Brainiac 5 avoided explaining the situation to Superman to prevent altering his future and because of his own shame. Superman turns away from him, furious.
Brainiac 5 reviews recordings of the battle and Shrinking Violet gives him a pep talk. He confesses that he wondered if somehow Brainiac 1.0 might corrupt him, or if some of that evil might lie within him. Shrinking Violet encourages him to move on and the genius catches a glimpse of the map in the recordings, leading to the Kandorian temple. The Legionnaires go there and Brainiac 5 realizes the Messenger is hidden beneath the temple. The Legionnaires fly down into a tunnel but the Messenger launches crystalline growths at them in automatic defense, while Imperiex and Validus fly after them. They manage to capture the other Legionnaires while Superman and Brainiac 5 fly ahead and get to the Messenger. In the process, Superman's suit is damaged and he loses his powers. Imperiex contacts them and demands that they give up the Messenger or he will kill their comrades.
The two heroes disagree on what to do next: Brainiac 5 advises the destruction of the Messenger since Superman can no longer defend it, while Superman wants to use it to save the Kandorians. Superman doesn't trust Brainiac 5 and takes the Messenger to the Kandorians, but they insist that he has already saved them, as he gave them hope in the 20th century to rise above the initial chaos of their relocation and create a new civilization.
Brainiac 5 goes back to the Kandorian temple and considers the images of Brainiac 1.0. He then bypasses the security protocols on his own racial memories and confronts the programming of the original Brainiac. It willingly gives up the control protocols for the Messenger and says it will open up Brainiac 5's mind to new possibilities. Brainiac 5 takes the information and flies off.
As Imperiex prepares to destroy the Legionnaires, Superman and the Kandorians arrive. None of them refuse to surrender, and they attack despite the lack of powers. Imperiex easily holds them back… until Brainiac 5 arrives and transforms Kandor's artificial sun from red to yellow. Not only does Superman regain his powers… but so do all of the Kandorians. Imperiex and Validus hastily teleport out without the Messenger.
Brainiac 5 explains what happens and then offers Superman a way to keep his promise. They travel to the location of Krypton, where there's nothing but debris. They then use the Messenger to recreate the planet, return Kandor to the surface, and then enlarge it.
Back aboard the Legion Cruiser, Brainiac 5 erases Superman's memory of events so that it doesn't interfere in his destined future. As the Legionnaires leave, Brainiac 5 briefly considers the situation… with an evil glimmer in his eye.
Making his first official Justice League appearance, Brainiac is another long-time recurring Superman foe from the comics (first appearance - Superman July 1958). A humanoid computer created by the computer tyrants of an alien planet, Brainiac possesses implacable intelligence and his evil knew no bounds, but he lacked any fashion sense whatsoever - he wore a pink tunic and short pants which has been immortalized in Challenge of the Superfriends and Cartoon Network parody ads of same. Brainiac was best known for having shrunk an entire Kryptonian city, Kandor, and tucking it away on his spaceship. Brainiac briefly became even more computer-like pre-Crisis, and then got retconned post-Crisis as a Coluan scientist who worked for the computer overlords and took over the body of a sideshow mentalist, the Amazing Brainiac.
Just to make things even more confusing, in Superman: The Animated Series, we got a new Brainiac (in "The Last Son of Krypton"), who was the computer system on Krypton and hid the impending disaster from the Council, then escaped at the last moment, made his way to Earth, and battled Superman on numerous occasions. It is that Brainiac that we see here.