In the aftermath of the attack on the wedding at the Kent barn, Lana surveys the wreckage and Clark arrives. He's been unable to find Chloe or Doomsday, and explains that there was an ultimate destroyer from Krypton that his father's AI warned him about. He tells her to get some rest but she wants to go the Isis Foundation to check Chloe's records. Clark is reluctant to involve her but Lana insists that Chloe needs both of them. They hug and Lana promises to call him as soon as she finds anything.
As soon as Lana is gone, a glowing light appears in the barn and an armored figure wielding a large axe appears. He cuts open Clark's chest with his ax and knocks him to the floor. He swings at Clark but a teenager magnetically pulls his axe away. Another newcomer, a woman, telepathically paralyzes him while a third teen hits the villain with lighting. The first teen removes a ring from the attacker's figure, sending him back where he came. The teen then says it's an honor and a privilege to meet Kal-El, and they identify themselves as the Legion from the 31st century.
The girl, Saturn Girl, warns that it will take a while for Clark to heal from the injury. The Legion tries to avoid telling Clark too much of his future but say they're his friends. The leader, Cosmic Boy, says that they came back in time to help Clark and now they're leaving. Clark demands an explanation. Cosmic Boy reluctantly explains that the man with the axe was the Persuader, part of the Human Supremacist Movement, a group of Earthlings that hate aliens, including Clark. The Persuader stole a Legion ring and broke into the Time Institute to come back to the 21st century and kill Clark. Cosmic Boy explains that his influence will reach beyond Earth and his presence will teach Earthlings to accept humans. The woman, Saturn Girl, notes that they're all aliens and that they must now leave. However, Cosmic Boy spots the Phantom Zone crystal and knows from his history that it was used to extract Brainiac from a human. They realize that Brainiac hasn't been destroyed yet.
In the Arctic, Davis lays in his human form, while Chloe is standing nearby. He approaches her but discovers that her eyes are silver. She grabs him and notes he's undamaged. He doesn't explain and "Chloe" explains that Brainiac now inhabits her body. Davis tries to get through to Chloe but Brainiac says he's not even human. Brainiac explains how he was created by Kryptonian geneticists and no longer needs camouflage abilities, and he needs to incubate in his Kryptonian chrysalis for 12 days. Once that has occurred, everything that is Davis will be stripped away leaving rage and power. He refuses to hurt anyone but Brainiac tells him he has no free will and will soon become… Doomsday.
Clark tries to explain that he's already defeated Brainiac, but the Legion knows that today is the day Clark defeats Brainiac. He realizes that Chloe is Brainiac's host and tells them to go back to the future. The Legion warns that if Brainiac isn't defeated, they have no future. However, with the crystal destroyed there's no way to free Chloe and Clark has no choice but to kill her. Saturn Girl gets Chloe's name telepathically from Clark's mind.
The next day, the Legion flies after Clark as he runs away and intercept him. He insists he won't kill anyone and that he was heading north to see Jor-El. Cosmic Boy explains that they've never heard of Chloe Sullivan in their future, and Lightning Lad concludes she probably didn't survive. Clark superspeeds away again and Lightning Lad wonders why Clark is so different from the one they know.
Saturn Girl goes to the Isis Foundation and explains to Lana that she's from the future and what has happened to Chloe. She warns that they can only stop Brainiac by killing its host, and they need Lana to convince Clark to kill Chloe. Lana refuses and Saturn Girl talks about the stories of Lana she's read and the incredible things she'll go on to do. She knows that Lana understands sacrifice because of all she's sacrificed herself, and knows what Lana plans to do next. Saturn Girl insists that Lana will realize that killing Chloe is necessary.
Cosmic Boy and Lightning Lad search Chloe's apartment and find notes on the Isis Foundation. They wonder if Chloe's death may have inspired Clark to fly.
At the Fortress, Clark calls out for Jor-El but Brainiac tells him that Jor-El is finally gone and it holds all of the information. Clark tells Brainiac to release Chloe but it refuses, saying it feeds on knowledge. Brainiac talks of Doomsday annihilating the planet and then taunts Clark, telling him to kill it by killing Chloe. It's confident that Clark won't, then casually throw Clark across the chamber and leaves. Clark goes after Brainiac, unaware that Davis is in a chrysalis nearby.
All three Legionnaires consider their options and Lightning Lad suggests that they kill Chloe themselves. Meanwhile, Clark goes to Isis and brings Lana up to speed about Brainiac. She's searching for power surges and tells him what Saturn Girl said about killing Chloe. Clark wonders about whether he's risking the world to save Chloe, but Lana says the Clark she knew would never doubt himself.
At the Daily Planet, Brainiac/Chloe taps into the computers and hypnotizes everyone watching the screens. Lana detects the power surge and identifies it as coming from the Daily Planet The Brainiac pattern appears on the screen, taking control of Lana.
The Legion arrives at the Daily Planet and Brainiac repels Saturn Girl's telepathic assault. Lightning Lad and Cosmic Boy combine their powers to hit Brainiac with an electromagnetic pulse. Saturn Girl detects low-level brain activity from Brainiac and warns they don't have much time. They realize that Brainiac is downloading the knowledge from everyone entranced by the computers. They place Chloe's body on a table and Lightning Lad prepares to kill her with a letter opener. He can't bring himself to do it and Cosmic Boy takes the knife. Before he can deliver the killing blow, Clark arrives and stops him. Saturn Girl says Chloe isn't there any more and they insist they must strike now. Clark says if they believe in him, his principles would mean they'd never kill. Saturn Girl detects a faint mental pattern from Chloe, confirming Clark's beliefs.
They take Chloe to the Kent barn and Clark says they have to work together. Saturn Girl connects Clark telepathically with Chloe. Cosmic Boy tries to extract the nanites magnetically while Lightning Lad shorts them out. Clark promises Chloe they're going to get rid of Brainiac, but her body starts to convulse as Brainiac comes on line. Cosmic Boy and Lightning Lad go to work and they extract the nanites.
At the fortress, Davis wakes up. Across the globe, everyone ensnared by Brainiac comes out of their trance. At the barn, Chloe wakes up, back to normal.
Later at the Talon, Clark visits Chloe as she packs to go see the injured Jimmy in Star City. Chloe wonders if Doomsday was powered down with Brainiac. Clark asks about what she remembers and Chloe notes that she still knows Clark's secret. She thanks him for not giving up on her, but figures that he would make the best choice for the world even if it meant sacrificing her. Clark says that as long as he's around, that will never happen.
Saturn Girl meets with Lana at the Clark farm while the others are outside fixing the barn. She admits they were willing to take the easy way out but Clark never gave up. Lana asks about her and Clark and Saturn Girl says they'll have to discover that for themselves. However, she does tell Lana that she has a destiny all her own.
Clark and the others finish repairing the barn and Lightning Lad is admiring Clark's first baseball and wants to keep it as a souvenir. Clark "signs" it with heat vision and Saturn Girl arrives with the nanites, compressed into a ball. They plan to take it back to the future. Cosmic Boy apologizes for doubting Clark and vows to preserve life at all cost in the future. They give him a Legion ring and tell him it will take him to the future whenever he wishes. Clark says he plans to stay in the present for the time being. As they prepare to leave, Cosmic Boy warns him to be careful in the days ahead. They activate their rings and return to the future.
Out on the porch, Clark examines the ring and Lana comes out. She realizes the Legionnaires have Clark as a role model, and he says that he'll be known throughout the galaxy a thousand years in the future. He's worried he won't live up to that and Lana assures him that he will, but has to do it on his schedule rather than theirs. Lana says it doesn't matter what they know of her future because they make their own destinies.
In the Fortress, Davis emerges from his chrysalis, transformed into Doomsday.