Brainiac 5 is engaged in a game of chess within his own mind, playing the remnant of programming belonging to the original 20th century Brainiac 1.0. Brainiac 1 tries to tempt Brainiac 5 into unleashing his untapped potential and bringing order to chaos. Brainiac 5's virtual image attacks his descendant, but upon driving it away discovers that Imperiex has left a bit of his own programming inside of Brainiac 5's memory systems. Brainiac 5 attacks him as well... and wakes up in the real world.
Imperiex is assembling his forces for a final assault on the Legion and then Earth, as a prelude to his conquest of the universe. The entire Legion and the Substitute Heroes have assembled to oppose him. Kell-El believes that Brainiac 5 can't be trusted: he's from the future and knows that the Coluan eventually goes evil. Superman insists that they try to save his friend and alter history. A Legion team then prepares for training in the simulation room, with Brainiac 5 at the controls. Brainiac 1 gains more power, appearing to Brainiac 5 in the real world through his senses. Under Brainiac 1's prodding, Brainiac 5 becomes more and more robotic and increases the danger level of the programming. When the Legionnaires start to go down, Superman bursts into the control room and manages to get Brainiac 5 to snap out of it. Brainiac 5 goes to his quarters and later Superman visits him to get an explanation. Brainiac 5 asks Superman to do whatever it takes if he goes out of control once more, and Superman reluctantly agrees.
Imperiex launches his attack on the Legion and Superman confines Brainiac 5 to quarters. The Legion split into two teams to defend the cruiser and attack Imperiex, but both groups are on the verge of defeat since Imperiex has programmed his Dominator troops with counters to the Legion's powers. Kell-El has gone off on his own to attack Imperiex but the galactic tyrant quickly overwhelms him and prepares to end his life. Brainiac 1 is still "talking" to his ancestor and Brainiac 5 finally gives in, assumes his battle form, and emerges to single-handedly shut down the entire Dominator fleet. Imperiex retreats with Validus but is satisfied with the outcome: Brainiac 5 has started to give in to evil and will soon join forces with Imperiex.
Superman vows to keep a close eye on Brainiac 5 despite the fact the latter assures them he is in control. Brainiac 5 retreats to his quarters but is easily able to spot Lightning Lad and Chameleon Boy when they use cloaking belts to keep an eye on him. He then gives in once more and renders them unconscious, then goes to the bridge, defeating all Legionnaires along the way. Superman is waiting outside and the transformed Brainiac 5 tries to run him over with the cruiser. Superman catches it and Brainiac 5 emerges in battle form to battle the Kryptonian. Superman subdues him but Brainiac 5 reverts to his more "human" self and begs Superman for mercy. It's a ploy, however, and the transformed Brainiac 5 renders Superman unconscious with a kryptonite beam then places a headpiece of the same material on Superman and leaves him floating in space.
The Legionnaires rescue Superman and remove the headpiece, but he is on the verge of death from kryptonite poisoning. They track Brainiac 5 as he travels to meet Imperiex and join forces. Imperiex opens a hailing frequency to the Legion and boasts of his victory, but Brainiac 5 turns against him. The Coluan transforms Validus into digital information, eliminating him. Imperiex tries to attack him but Brainiac 5 immobilizes him and then "deletes" him once and for all as he has served his purpose. Kell-El is furious since that was his objective. The transformed Brainiac 5 takes control of the Dominator armies and announces that he now plans to bring order to a chaotic universe. He departs for his homeworld of Colu while Lightning Lad announces that Superman has succumbed to kryptonite poisoning and is dead.
(to be continued...)