The improved Brainiac/Brainiac 5, "Brainiac 6," attacks the planet Thanagar and digitizes first its winged warriors and then the planet itself. The Legion watches as Brainiac 6 completes the digitalization and then approaches Colu. The Legion tries to warn the Coluans but they are not interested in help. The Legion tries to intercept Brainiac 6 while honoring the deceased Superman and sending his body into the sun.
Brainiac 6 engages the Coluans who are able to protect themselves against him. They teleport him into the council chambers and prepare to reprogram of him by using matter transmission technology.
Kell-El is in his quarters mourning the loss of… Imperiex. He feels useless now that his life's purpose has been taken from him. Timber Wolf berates him for forgetting everyone else but Kell-El warns that he's seen the future and Brainiac 6 wins. He immobilizes Timber Wolf and storms out, saying he was never a member of the Legion. Kell-El collapses in pain and realizes that Superman is alive. They conclude Superman is in a state of suspended animation while trying to overcome the kryptonite radiation. Saturn Girl links with Kell-El and determines where Superman is.
Brainiac 6 reverses the programming attempts and assaults the Coluan hive mind. He takes control of it and prepares to use all of its people to bring order to the universe. They fly off into the galaxy and digitize planets and their inhabitants.
Superman's coffin is falling into the sun but Kell-El rescues him just in time and flies him back to the Legion cruiser. They then give Superman a transfusion of Kell-El's kryptonite-immune blood. The Coluans go to digitize the Legionnaires but they've used Computo to make themselves immune. They try to appeal to Brainiac 6 but he ignores them and analyzes their defenses as they attack.
Superman awakens but is still too weak to attack. Meanwhile, Brainiac 6 draws the Coluan forces into a single gigantic body. Colossal Boy is the first to attack but Brainiac 6 negates his protective belt and digitizes him. Superman suggests they get into Brainiac 6's programming but on their terms. He has Saturn Girl project him into Brainiac 6's mind along with Kell-El so they can work together. They appear within Brainiac 6's mindscape and find Brainiac 5 all but dismantled. The original Brainiac 1.0 appears and starts to deprogram them.
The Legion falls one by one while Saturn Girl sends a mental message for Superman and Kell-El to merge into one mental force, the "Supreme Superman." The conglomeration assaults the Brainiac 1.0 image while Brainiac 6 takes control of Lightning Lad's arm and uses it to knock out the remaining Legionnaires. Brainiac 6 prepares to dispose of the Legion cruiser, with Superman and Kell-El's physical bodies. Supreme Superman insists that Brainiac 5 was a true hero and as they go down, Brainiac 5 reassembles himself and retakes control. Brainiac 1.0 tries to dispose of them all but Brainiac 5 casually deflects the blasts, generates dozens of self-images, and destroys Brainiac 1.0, seemingly for good. All of the Coluans are released and everything that was digitized is restored. A new more human Brainiac appears before them.
Later, Superman checks up on Brainiac 5 and assures him that he is a hero, but Brainiac 5 decides to leave the Legion until he can sort out his new feelings as a human. At Legion Headquarters, Kell-El prepares to return to the future and thanks the Legion for helping him mature. They make him an official member of the Legion, while Triplicate Girl's third body is restored when the future where it was destroyed is restored.
And somewhere out in space, the components of Brainiac 1.0 start to assemble themselves…