- The aftermath of Doomsday's attack on Chloe and Jimmy's wedding leaves Clark in shock, but before he can search for the kidnapped Chloe, an evil being, known as The Persuader, appears and attacks him. Rokk, Imra and Garth, also known as The Legion, step in from the future to help vanquish the Persuader and the group realizes Brainiac has taken over Chloe once again. Meanwhile, up at the Fortress, Chloe, as Brainiac, informs Davis he is Doomsday and was created to kill "the other Kryptonian" and destroy the world.—Anonymous
- Lana Lang arrives at the wrecked barn, crying, when Clark arrives. He reports that he has been unable to locate Chloe or the thing that took her. He tells Lana that Jor-El warned him about an "Ultimate Destroyer." Lana decides to go to the Isis Foundation to help look for Chloe. When she is gone, there is a flash of light and a masked man with a big metallic, glowing axe appears in the loft and he smashes his axe through a large trunk in the loft. Clark confronts him and asks who he is and the man attacks a surprised Clark, wounding him in the side with the axe.
They continue to battle just as three more people appear. One man uses his power over magnetism to disarm the attacker, a blonde woman in red clothes practices some sort of telepathy, and another man strikes the attacker unconscious with a bolt of energy from his hands. The first hero takes a ring from the fallen attacker's hand and the attacker disappears.
Clark is stunned and finally asks who his three saviors are. They call Clark "Kal-El" and explain they are the Legion, from the 31st Century. They introduce themselves: the woman is Imra; the younger man is Garth, who is very excited to meet Clark and tells him that they know his future as a great superhero; and the leader is Rokk, who cuts Garth off from revealing too much information about Clark's future and says that they came to save him from the man who attacked him. He was the Persuader, who stole one of the Legion flight rings to come back in time and kill Clark. Rokk is ready to take his team back to the future, but Clark says he doesn't care about their team or the future because his best friend is missing. Imra reads Clark's mind and learns that he is thinking about a woman named Chloe Sullivan. Garth knows that they are in the day in history when Brainiac was defeated, but Rokk notices that the Martian crystal needed to trap him, which Clark was keeping in the trunk smashed by the Persuader, is now broken. He decides that they cannot leave because they must help Clark to finally defeat Brainiac.
Davis Bloome, half-naked, wakes up in the Fortress of Solitude. He sees Chloe and is relieved to find her there. However, Chloe approaches him, acting strangely. She examines Davis and says that he appears undamaged. Davis asks what happened to her, and she says that she is not Chloe, but the Brain InterActive Construct. Brainiac explains that Davis is merely the human guise for the Ultimate Destroyer and must be locked into a chrysalis to fully and permanently transform him.
Clark is super-speeding to the Fortress to ask Jor-El to help him find Chloe. The Legion members catch up with him through flight. They tell him that, since they have never heard of Chloe Sullivan, she must die in the process of defeating Brainiac. Clark angrily declares that Chloe won't die and speeds away.
Imra goes to the Isis Foundation and meets Lana. Lana initially thinks she is a meteor freak seeking assistance, but Imra starts to inform her of Brainiac taking over Chloe and asks her if she will convince Clark to kill Chloe. Lana insists she would never ask Clark to kill anybody. Imra tells Lana that she thought, based on what she knows of history, that Lana would help.
Imra meets up with Rokk and Garth, where they go through Chloe's work at the Isis Foundation. They note that she has gathered many years worth of information on people with abilities. They cannot figure out the reason why, if Chloe Sullivan is so important to Kal-El, they have never heard of her in any of their known history. The Legionnaires conclude that they must stop Brainiac themselves.
Clark goes to the Fortress to speak to Jor-El, but finds it corrupted, with Brainiac in Chloe's body absorbing information from the crystals. Brainiac reveals his plan to take all of Earth's information and knowledge, then have Doomsday destroy it. Clark grabs Chloe/Brainiac and shoves him against sharp crystals, but he can't bring himself to kill Chloe, despite Brainiac's taunting. Brainiac says he chose Chloe's body because he knew Clark wouldn't harm her. He then picks Clark up, tosses him across the Fortress, and speeds away. Meanwhile, elsewhere in the Fortress and unbeknownst to Clark, Davis is locked in an ice chrysalis.
Clark explains to Lana how Brainiac has returned and that some people are convinced the only way to stop him is for him to kill Chloe. Lana tells him that a woman came in before saying the same thing. Clark wonders if killing Chloe might really be the only way. Lana is shocked by this and points out that the Clark she knows would insist that there would be a way to save both Chloe and the world. Just then, the computer indicates a power surge. Lana pinpoints the surge to the Daily Planet. Brainiac's symbol suddenly appears on Lana's computer screen, hypnotizing her. Clark calls her name, but she does not respond, so he rushes off to the Daily Planet.
Chloe/Brainiac arrives at the Daily Planet to absorb the information stored there. He hacks the wiring and slowly steals everybody's knowledge by hypnotizing them with his symbol displayed on every computer screen. The Legionnaires arrive and, while Imra distracts him as he is about to attack, Rokk and Garth attack Brainiac with an electromagnetic blast, temporarily disabling him. Garth reveals a knife and is ready to stab Chloe/Brainiac, saying he took an oath to protect anyone and is ready to do that. But he cannot bring himself to follow through, so Rokk takes the knife and is about to wield it when he is stopped by Clark. Clark tells them that Chloe is still inside, and that he believes he can defeat Brainiac without killing anyone. He asks Imra if she can connect with Chloe. Imra attempts it and can hear Chloe asking for Clark's help.
Clark and the Legion take Chloe, still unconscious, to the barn, a long way from computers. Clark encourages the others to work together to take Brainiac out of Chloe: Garth will create an electric burst to keep Brainiac at bay, while Rokk will use his magnetism to pull the metallic nano-bytes out of Chloe's body, and Clark and Imra will hold her down and connect with Chloe. When Brainiac re-activates, Garth blasts him down while Rokk pulls him out, in the form of a black metallic sphere, from Chloe's mouth. Chloe regains consciousness and says that she is fine and can tell that Brainiac is gone.
Back at the Fortress, Davis awakens.
The next day, Clark visits Chloe at her apartment, to find her memory completely restored, including his abilities and his alien origins. Chloe tells him that the next time something like this happens, she wants Clark to do what is best for the world and not for her, because if it were the right thing, she'd understand. Clark tells her that won't happen as long as he's around, and Chloe looks at him worriedly. She continues packing her things because she is going to visit Jimmy and Lois in Star City.
Lana and Imra meet again at the Kent house, and Imra refrains from telling Lana details of her future, but tells her she has a special destiny. As Clark, Garth and Rokk fix the barn, Imra comes in with the Brainiac sphere in her hands. Rokk says that they will try to re-program Brainiac into something useful, and Imra hopes that "Brainiac 5" will be a little more friendly. Clark gives Garth his legendary baseball, which when young, he had hit to the other side of Smallville, and burns his initials on it with his heat vision. Rokk gives Clark a Legion ring only good for time travel, and the Legion takes Brainiac back to the 31st Century with them.
Later, Clark and Lana discuss the future and how their lives may turn out, whether or not they are together.
At the Fortress, Davis has morphed into Doomsday and broken free of his ice chrysalis.
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