Lois arrives at Clark's doorstep with her goods and announces that she's taking him up on his offer to move in. Clark says it's not a good idea for them to be working and living together but Lois is enthused about her idea. She hands him a package that she found for him on the doorstep, a package with no return address. Clark opens it and finds the blue Kryptonian crystal inside. He picks it up and examines it and it starts to first glow and then buzz. As the farmhouse starts to shake, he tells Lois to run but she grabs him and the two are caught within a Phantom Zone glass square, which rockets out through the window and up into space.
Chloe arrives at the farmhouse and discovers the destruction. She finds the crystal and pockets it, and realizes Clark and Lois are gone. Tess comes in and wonders what happened. Chloe makes up a story about a bird flying through the window, which Tess doesn't believe, and she asks for the crystal. Chloe says she doesn't have it but Tess says that she used a frequency detector to track it there. Chloe continues to deny any knowledge of it as well as Clark's involvement, and Tess wonders why she's going to such lengths to protect Clark.
An injured Clark wakes up in the Phantom Zone under two suns and without his powers. He locates an injured Lois nearby, and she insists that aliens have abducted them.
Chloe goes to Isis and tries to contact Oliver, who is in South America. Davis comes in and asks to see her despite her previous request for him to back off. He explains that he's been trying to identify his birth parents but hasn't had any luck. He wants Chloe to help, as he hasn't been able to find out anything about the first three years of his life.
Clark keeps Lois moving across the landscape to stay ahead of the Phantoms in the Zone. When she starts to panic, Clark helps her to get a grip. A robed figure attacks them and knocks Lois unconscious, then grapples with Clark. He sees her bracelet with the "S" symbol and realizes it's his cousin Kara. Kara explains that Brainiac sent her there and says the Zoners will scent their blood. She tells Clark that Jor-El left them an escape route, but she's been unable to take it since more Zoners could pass through to Earth, as they did when Clark escaped years ago. Clark insists that Lois needs to go back since she has nothing to do with Jor-El or Krypton, but Kara ruthlessly tells him that Lois' life isn't worth endangering Earth. Clark insists and wonders when Kara became so ruthless, and she explains that she's been trapped there with no hope of escape. She gives him a knife as Lois wakes up.
Chloe catches up to Oliver at his private jet in Metropolis and shows him the Kryptonian crystal. She wants him to help her by stealing a frequency generator to power up the crystal to get Cark and Lois back. Oliver wonders how she knows her plan using alien technology will work but Chloe says she knows what she's doing. He wonders what he's hiring but agrees to help him. He agrees and then becomes more enthusiastic when he learns he'll be stealing from Tess Mercer, his ex-girlfriend and current rival.
In the Phantom Zone, Clark sends Kara ahead to get Lois through the portal while he holds off the Zoners. Kara takes Lois to an underground chamber with an altar embossed with the "S" symbol. She cuts her palm and uses her blood to activate the device, but Lois hears Clark fighting outside and refuses to leave her. Kara shoves her through then turns as a Phantom flies into the cave. It slams Kara against the wall where she's buried in debris, and then flies through the portal.
Lois wakes up on Earth but before she can do anything the Zoner flies into her body and takes her over. The possessed Lois goes to the
Daily Planet and starts going through old newspapers. Tess finds her and asks what she's doing. The Phantom says that she's looking for her son, the child of General Zod, and talks about Kal-El arriving in a Kryptonian spacecraft as a baby and how her son was on the spaceship as well. Tess, intrigued, tries to make a deal in return for her help but the Phantom suspects she's up to something and leaves.
Clark, injured, finds Kara and tries to free her without success. She tells him to leave but he refuses to leave her to the Zoners.
Chloe arrives at her apartment and gets a message from Oliver saying he's nearing the target. The possessed Lois comes in and Chloe hugs her, relieved, but quickly realizes something is wrong with her. The Phantom says she is Faora, the wife of General Zod, and has taken Lois' body as a vessel for herself. Faora chokes Chloe and demands to know where her son is. Chloe doesn't know what she's talking about, but Faora sees her file on Davis and recognizes him, then leaves.
In his Green Arrow costume, Oliver breaks in to Lex's manor and prepares to steal the frequency generator. Tess catches him, holds him at gunpoint, and demands to know who he is and whom he's working for. He immobilizes her with a paralytic arrow-dart and takes the generator.
Faora goes to the Metropolis hospital and embraces him, then admits she's surprised that he's helping injured earthlings. She wonders if he caused their injuries and says that she's his mother.
Oliver goes to Isis with the generator and gives it to Chloe. She uses it to activate the crystal and goes into a trance. When Oliver tries to intervene, she smashes him unconscious.
Clark is still trying to free Kara, who tells him to take the portal and go. He refuses, saying she's his family. A portal forms above Clark and yanks him upward. He manages to hold out long enough to reach out to Kara and tells her to take his hand. She hesitates but finally takes it and the two of them are pulled through and appear at Isis. Chloe tells them what happened and Kara explains who Faora is. Clark tells Kara to go to John Jones with the Metropolis police and get a crystal while he deals with Lois.
In an examination room at the hospital, Faora tells Davis that she and Zod sent him to Earth as genetic matter attached to Kal-El's spacecraft. The genetic matter was made up of Krypton's strongest life forms and designed to evolve into the ultimate destroyer. She says that Davis is too weak then rams a metal strut through his chest. He collapses to the ground, dying, and she tells him that what doesn't kill him makes him stronger. She leaves the room but says that she'll be back when he's ready.
Outside, Clark grabs her and asks what she's done. Faora tells him that her and Zod's creation will destroy Clark's new home world. He tries to get through to Lois but Faora mocks him then realizes he's hesitating because of his feelings for Lois. She shoves him out through a wall to the street below, then superspeeds down to deliver the final blow. Kara arrives and uses the crystal from John to pull Faora's phantom essence into the crystal and contain it.
Upstairs in the examination room, Davis sucks in air and comes back to life.
The next day, Lois believes that the entire thing from the time she touched the crystal is a dream, one where she imagined Clark as a hero. She reveals that Tess gave her a raise, making Clark suspicious. Lois says she won't be moving in since she can afford a new place with the raise. Tess summons Clark to his office and asks him about the Kryptonian spacecraft that Faora mentioned while in Lois' body. Clark says he doesn't know anything and Tess shows him his boot print from the farm's driveway... and a matching boot print from the Arctic near where Lex disappeared. She wants to know what Clark knows of Lex's disappearance but he simply says that a lot of people wear work boots. He says she should fire him if she doesn't believe him but Tess says she wants him to trust her and realize they're on the same side. She tells him to go but notes that someday the truth will come out.
Clark returns home to find Oliver there. Oliver tells him what happened to Chloe and wants to know what Clark is doing to stop Brainiac from possessing her. Clark says he's doing what he can but Oliver warns that if Chloe continues drawing on Brainiac's powers she'll be hurt... or worse.
Clark goes out to the barn and examines the Kryptonian blue crystal. Kara wonders if he'll use it to rebuild the Fortress but he figures it's too dangerous. Kara suggests that Clark tell Lois his secret: he knows she can be trusted or he wouldn't let Lois get so close. Clark doesn't respond and Kara tells him she's leaving Earth. While in the Zone she heard rumors that her city of Kandor may have survived Krypton's destruction. Clark offers to go with her but she says his destiny is on Earth and hers is to find Kandor and continue their bloodline. She shows him her necklace, with an "S" symbol on it, and says he'll always be close to her heart. She then turns and flies away.
In the examination room, a pensive Davis takes a knife, braces himself, and then stabs himself in the chest. The blade shatters on his now impenetrable skin.
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