Jimmy serves Chloe breakfast in bed and asks about Lana, who they haven’t heard from yet concerning the wedding. Chloe’s seems to momentarily blank on Lana’s name and jimmy observes that she’s been getting increasingly forgetful the last few weeks. He talks about their dancing at the engagement party and Chloe remembers back to their dance. However, as she thinks back the entire memory starts to fade away in bursts of computer code, leaving Jimmy as a blank-faced mannequin. Chloe snaps back to the present… and doesn’t recognize Jimmy at all. Cowering back in the bed, she tells him to get out.
Jimmy goes to the farm to get Clark’s help, explaining he managed to calm Chloe down by showing her pictures of the happy couple together. However, she still doesn’t remember their engagement or Jimmy himself. Jimmy wants Clark to talk to Chloe since Clark has known her the longest. Meanwhile, Chloe has gone to Metropolis General Hospital to do research on brain disorders and runs into Davis. He says he doesn’t want her to research his past any more but realizes that she’s having problems. He offers to help and she says she isn’t feeling well, and says she’ll talk to him later.
Clark finds Chloe at Isis as she’s going through a book on memory disorders. She quickly hides the book and rattles off information about Clark and Jimmy, but Clark realizes that she’s going by memory. He goes into Chloe’s hidden computer chamber and discovers that she’s pulled up research on everyone she’s ever known: Clark, Jimmy, Lionel, Jonathan, and Martha. She finally admits that something is wrong and that Brainiac is making his move.
Davis stops by Chloe’s apartment and runs into Jimmy, and says he won’t be attending the wedding because he’s scheduled to work at the hospital. He tells Jimmy to be sure and take care of Chloe.
Chloe and Clark go to the Kent barn where Chloe draws a recurring symbol of the code she sees whenever her memories fade. Clark recognizes it as the Kryptonian symbol for “Doom. Despite the fact it teleported him to the Phantom Zone, Clark wants to use the Kryptonian crystal to recreate the Fortress and the Jor-El AI program. Chloe doesn’t want him to take the risk and says her life has changed for the better by knowing him. However, as she remembers the night when she first saw Clark use her powers, the same coding sweeps through her mind, erasing that memory. As she snaps out of it, she no longer remembers that Clark has super-powers. They figure out that her memories disappear when she tries to remember them. He decides to recreate the Fortress and tells Chloe to trust him and wait there. He convinces her to stay there and gives her a photo album of the two of them together so she can try to hold onto her remaining memories.
Clark goes to the Arctic and looks on as the crystal rebuilds the Fortress. Meanwhile, Jimmy arrives at the barn with a photo album himself and Chloe together. He realizes she still doesn’t remember him and tells her he’s made an appointment for her to see a neurologist. He doesn’t understand why Clark left her there alone and asks her to trust him.
Clark talks to the Jor-El program and accuses it of betraying him. He says that he’s learned to care for everyone, not just his friends and family, and Jor-El praises him for having matured. Clark says it’s time for “Jor-El” to trust him and he needs it to help Chloe. Jor-El explains that he can reverse the memory loss but the process is unpredictable and doesn’t know what might happen with the Brainiac program.
Chloe undergoes a MRI at Metropolis General and the Brainiac program wipes the electronic scans. Chloe remembers meeting Clark for the first time at his barn loft and talking about their mutual love of books. Her teenage self gives Clark a kiss, saying she knows he wants to so she figures she’d get it out of the way. However, everything in the barn starts to come apart and fly up into the sky, and Chloe realizes the Brainiac program is active again. She grabs Clark’s hand and tries to get him into another memory, of Dark Thursday at the
Daily Planet when Brainiac wiped out the world’s power supply. However, that memory starts to deconstruct as well and Chloe realizes there’s nowhere to hide her memory of Clark. The memory is swept away in a burst f Kryptonian code and Chloe finds herself faced with… Davis. The memory of Davis takes her hand to reassure her, and Chloe wakes up in the MRI chamber.
Chloe goes to find Davis as he’s returning to the hospital and tells him that she doesn’t trust anyone else. Meanwhile, Clark returns to the Talon as Jimmy makes calls to try and find Chloe. Clark prepares to leave, telling Jimmy to call John Jones for help, and Jimmy thanks him for being there. As Clark goes downstairs, Davis brings Chloe in but Chloe no longer remembers her friend. She doesn’t remember Jimmy when he comes downstairs. Davis is forced to sedate her and wonders why Chloe remembers him. Davis leaves Chloe with them and goes, and Jimmy goes to get Chloe’s belongings to take her to the hospital. As soon as she’s gone, Clark takes Chloe to the Fortress and asks Jor-El to restore her memories… except for those of Clark’s superpowers and Krypton. Jor-El agrees and Clark apologizes to Chloe but believes it’s best for her that she doesn’t remember his secret. As Jor-El restores her memories, a drop of black liquid drops from Chloe’s eyes and enters the surrounding computer crystals.
Later, a recovered Chloe and Jimmy plan their wedding and she admits she doesn’t remember anything that happened to her. Clark arrives and admits it’s a miracle, and Jimmy wonders if the sedative might have done something to stop the memory loss. Clark hints that he can make a superspeed trip to Metropolis for their flowers and Chloe has no idea what he’s talking about. She goes to Metropolis for the flowers and Davis meets her. He says that he lied and he doesn’t want to be at the wedding because he feels that Jimmy is the wrong man for her. When she insists that she loves Jimmy, Davis points out that he was the one she remembered, not Jimmy. He kisses her and she responds briefly, but then backs off and says she doesn’t have any feelings for her. Davis says that he’s not going to let her go, and will wait until she realizes her mistake.
Clark goes to the Fortress where Jor-El says that he’s proud of him for making the personal sacrifice. He identifies the “doom” symbol as the mark of the Ultimate Destroyer, a Kryptonian create that evolves to overcome any opposition. Clark figures that Brainiac was somehow trying to make contact the Destroyer, and Jor-El warns that it will soon succeed. Clark vows to deal with it as he’s dealt with everything else, and Jor-El assures him he’ll help.
Clark leaves, but the black liquid spreads throughout the Fortress. Brainiac boasts that he will soon destroy the House of El and that “Doomsday is coming.” The “doom” symbols appears on the Fortress as Brainiac takes control…
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