In Metropolis, Faora reads an article about the destruction of the tower. She's wearing her Kandorian tag and Clark finds her. He warns her not to reveal her alien nature in public, but she wonders how she can have any hope after the tower's destruction. Her only hope is Clark, who found her sister, Vala, who is now working at a bookstore and blending into human society. Vala insists that Clark will protect them but Faora isn't so sure. As Clark leaves to deal with a crime, Faora warns Vala that she can't fall in love with Clark and tells her to close up.
As Vala goes back into the bookstore to close up, someone apparently comes into the store. Vala turns but doesn't see anyone. As she closes the door and goes back into the store, a man grabs her and sprays her with gas, rendering her unconscious. Later, Vala wakes up and finds herself in a hidden laboratory contained within some kind of device, surrounded by two other similarly imprisoned Kandorians.
The next day, Lois is working on a story at the Planet when she gets a call from Amanda Waller. She quickly puts her special phone away as Clark comes in. When he wonders what's going on, she suggests they have a romantic dinner together. Clark agrees, but Faora arrives and asks for Clark's help. He claims that she's part of a story he's working on and gets her off to the side, where she explains that Vala has been kidnapped.
Oliver is in his office after exercise and finds Tess in his desk. She wonders why he's not worried about the destruction of the Solar Tower, and figures that he might be involved. Oliver denies it and Tess says that she doesn't believe him. She warns that someone at one of Oliver's subsidiaries is embezzling funds. Tess tells him to find who is responsible and put an end to it.
Clark goes to Vala's store and finds Zod there. The major tells Clark that he's dealing with it and he should go save humans. He blames Clark for driving a wedge between Zod and the others, and now they've abandoned him, someone is abducting them and leaving their crests behind. Clark refuses to give him his powers back and Zod attacks him, but Clark easily stops him. Zod recovers his composure and tells Clark to admit that he's turned against the Kandorians. Clark points out that Zod can't tell his own people because he doesn't know which ones he can trust, but Zod says that the blood of the Kandorians is on his hands.
In the hidden laboratory, Vala's abductor, Dr. Bernard Chisholm, removes his mask after locking her in an anti-contamination container. He explains that when he found them, he realized they want to colonize the planet. When she denies it, Chisholm says that he's going to gather proof and show the world so that the Kandorians are hunted down and exterminated. He then puts on his mask again and turns her around to show her a severed arm with a Kandorian brand. Then Chisholm goes back to work, cutting apart another Kandorian.
Oliver comes to see Chloe at her apartment. She's glad to see him but Oliver ignores her and looks around. He then turns up the music and embraces her, and explains that Tess might be listening. Oliver warns her that Tess' evidence indicates that Chloe is stealing from him. She says she was borrowing the cash to buy insurance for the entire planet.
Clark goes to see Faora and ask what happened to the other two Kandorians, and how Vala was connected to them. Faora explains that all three of them were cybernetic engineers who performed tests to recover the Kandorians' powers. She wonders if the tests are responsible for her abduction. Clark asks her to explain and Faora admits that they were experimenting on humans.
Lois goes to the restaurant where she planned to eat with Clark and orders for one. When she looks up from her paper, she discovers Dr. Chisholm sitting opposite her. He says that he has a story for her that will make her career: aliens are living among them. Lois doesn't believe it and tries to walk away, and Chisholm says that he's captured some of them. She admits that he's convincing and claims she's calling her editor on her cell phone, and goes outside. She then calls 911 but Chisholm follows her and takes her prisoner at gunpoint.
Back at his lab, Chisholm shows a manacled Lois blood samples that he claims proves his prisoners are aliens. When she warns that no one will believe him, he shows her the prisoners, including a cryogenically proven specimen: Vala. As he starts to freeze her, Lois tries to stop him and he reveals that his skull has been cut open and crudely stitched together. Chisholm says that he died of a heart attack and the Kandorians, including Vala, inserted kryptonite spikes into his skull as part of a process to bring him back. Now he can't stop thinking and his new thoughts are driving him insane. Chisholm warns Lois that the invasion has begun and they have to save mankind.
Clark and Faora go to the hospital and Faora explains that Vala and the others store cadavers from the morgue. Clark insists that it wasn't right and Zod should never have allowed it. Faora tells Clark that Zod didn't know, and insists that Clark has no right to pass judgment on her leader. She tells of how Zod risked his own life to save her during a battle. When Clark notes that Zod let Jor-El die, Faora insists that Zod has always considered Jor-El his friend. He admits that he might be wrong, and Faora warns that he doesn't know the man.
Zod goes to the Planet and secretly steals what he needs to pass as a mild-mannered reporter. He then goes to see a reporter, Molly Nichols, and asks her to help him find some information about alien conspiracy nuts. She gets him a box of letters, including all of the ones that Chisholm tried to send to warn of the alien threat.
Chloe takes Oliver to a secret storage container where she has gathered kryptonite weapons for the day that the Kandorians get their powers back and try to conquer the world. All of the IDs she's given them have tracking devices hidden in them. Chloe explains that they can't afford to trust Clark again. As they leave, Tess' man Lenkov takes photos of them.
Lois is working on her story when Zod comes in and frees her. He claims he's an FBI agent and goes to release Vala. Before he can stop the cryogenic process, Chisholm arrives and shoots him in the chest. He tells Lois to finish her story while Zod bleeds out. After Chisholm leaves, Lois gets free and runs to help him, putting pressure on the wound. He warns her to leave before Chisholm returns, but when she refuses, he wonders why. Lois says that it's what Clark would do, and Zod warns that his supposed FBI backup isn't coming. He tells her to save herself and Vala.
Clark and Faora talk to Dr. Flores, who works in the morgue, and ask if all of the bodies were recovered. He admits that one body, John Corben, was never recovered. He tells them that they'd have to talk to the attending M.E., Dr. Chisholm, who has been released for psychiatric reasons. Clark threatens to quote him as a source, and Flores explains that Chisholm said that he saw the body snatchers, claimed they were aliens, and had a heart attack. Then they brought him back to life. Clark convinces Flores to give him Chisholm's address.
Chisholm returns to the lab and discovers that Lois is gone. Lois ambushes him and knocks him into an electrical panel. As she tries to free Vala, Chisholm recovers and knocks her out. He sees Zod's Kandorian tag and realizes that he's an alien. Chisholm picks up his surgical gear and prepares to cut Zod open, ranting that he'll stop the invasion now. As he moves in, he hears a whooshing noise. Clark knocks him aside but Chisholm grabs his drill, swings it overhead, and inadvertently electrocutes himself. Clark is unable to go to his aid due to the kryptonite spikes present so he frees Vala and then runs to Zod's side. Zod says that Clark will get what he wants, but Clark insists that Jor-El's last wish was for him to save Zod. Zod admits that's something that Jor-El would have done, grabs his hand, and says that Clark can't save him. He dies and Clark takes one of the kryptonite spikes, cuts open his hand, and drips his blood into Zod's wound. There's a burst of light and Zod's wound heals.
Lenkov takes Tess to the container only to discover that it's empty. She tells him to find the weapons her money is being spent to purchase. Chloe is watching and is surprised to discover the weapons are gone. Oliver arrives and tells Chloe that he figured Tess was following him, and has hidden the weapons where she can't find them. Chloe demands to know where they are and wonders if they should tell Clark, and Oliver says they should… when the time is right.
At the Planet, Lois calls the laboratory to have one of Chisholm's blood samples examined. She then goes to her office and hides the sample in her desk, although Clark spots it. Lois notes that all of her evidence has disappeared, and the FBI has no record of an Agent Zod. Clark claims that Zod is deep undercover and offers to tell her what he knows, if she reveals what she has hidden in her desk. Lois concedes that a little mystery might be good for their relationship. Clark gets a call from Zod to meet on the rooftop and he makes a hasty exit. Once he's gone, Lois gets a call from Waller, thanking her for the blood sample. Lois checks her desk and discovers that the sample has been replaced with a white chess piece.
On the roof, Zod asks if Lois is well, and admits that she protected him. He realizes why Clark cares for her, and admits that he is a changed man. Zod wonders how Clark knew his blood would cure him, and Clark admits it was a guess. The major then admits that he trusts Clark now that he realizes he cares for the Kandorians. They shake and Clark leaves to deal with another crime. Once he's gone, Zod goes to the edge of the roof, embraces the sunlight, and then lets himself fall. Halfway down he gains the power of flight and soars into the sky, smiling.