On Kandor in the middle of war, Kara's father Zor-El takes her to a ship while warning that the Council has sealed all of the portals to prevent Zod from escaping. He gives her a crystal so she can come back to him while he remains to protect Kandor. On Earth in the present, Kara remembers as she flies through the sky, narrowly avoiding a jetliner. She then arrives in Washington D.C.
Chloe is working at the Daily Planet when Clark arrives and she informs him that the FAA spotted Kara. Jimmy shows up and they realize that he knows something, and he reveals that he showed her the video that pointed to the government. Chloe wonders why Jimmy didn't tell them but he notes that Kara trusted him with the secret.
Clark goes to Lionel who is familiar with the government's operations and their project Starhawk, which took an interested in Smallville after the second meteor shower. Lionel wonders if they may have found something that changed their minds, and tells Clark what he knows about Smallville.
Agent Walker is having his team analyzing the crystal from Kara's ship when Lex arrives and wants to know what he's found out. When Walker refuses to tell him, Lex warns that it's only a matter of time until he finds out. After he leaves, Walker continues the scan.
Kara is at a party in Washington using her superhearing to find a technician talking about the crystal. She comes on to him and after getting him in the backroom, convinces him to tell her about the crystal at their lab. She then superspeeds away to the lab and uses his (stolen) security guard to gain access. However, the crystal is gone.
Chloe goes to the Isis Foundation, which reaches out to meteor victims, and finds Lana there. Lana explains that she runs the foundation and asks Chloe not to tell Clark so he won't try to talk her out of it. Chloe doesn't believe her but Lana dismisses her concerns.
Kara goes back to the technician and demands he tell her where the crystal is. He insists it hasn't been moved and Clark arrives to tell her to back off. He takes her outside but Kara believes he betrayed her and stands by her father. She goes off to prove it to him and insists he's being selfish. When he refuses to let her leave she shoves him away and superspeeds away.
Kara returns to the Daily Planet where Jimmy finds her going through files on his computer. It turns out she's going through fied government information and finds a LuthorCorp defense contract subsidiary. When Jimmy sits down to help, Kara secretly superspeeds away.
At the Isis Foundation, Lana is running surveillance on Lex when Kara arrives at the manor and finds a hidden vault. However, she collapses when Agent Walker comes up behind her with a kryptonite set of handcuffs. He thinks she's working with Lex and has concluded that kryptonite adversely affects her. Lex comes in and Walker draws a gun on him. Walker believes Lex stole the crystal and he shoots him down with a tranquilizer dart then leaves with Kara. Meanwhile, Lana accesses the security tapes and sees the recorded image of Kara scanning the wall for the vault. She calls Clark to let him know where he is.
Lex is awake and contacting the government when Clark arrives to try and find Kara. Lex swears she's been taken to a lab in Virginia and wants to know why Walker would arrest her.
Back at the lab, Walker has strapped down Kara and kept her weakened with kryptonite. He then uses the Somerholt memory-scanning device by delivering the kryptonite solution directly into her veins. He picks up memories of Kara in 1986 visiting her Aunt Lara on Earth at the Kents' barn, sneaking through a portal from Kandor. Lara reveals that she's pregnant and Kara swears to protect her son. Walker is intrigued and scans at a higher concentration. He finds a new memory of Lara and Kara sneaking into the Kents' house while the couple are out. Kara suggests that Lara name her son Kal-El and takes a picture of Lara. They hide it behind a photo but are interrupted when Zor-El bursts in.
Walker's memory scan is interrupted when Clark rips his way in but is weakened by the kryptonite. He manages to knock Walker down and free Kara, but when he touches her he receives the memories of Zor-El sending Kara outside and then saying there's no reason for them to return. Zor-El asks Lara to stay with her and realizes she's pregnant, then says that Jor-El stole Lara from him. He says that they'll be together one day thorough his science, and Lara realizes he stole her DNA and put it in the crystal. Kara interrupts them and he wipes her memories. Kara flatlines from kryptonite exposure and Walker tries to kill Clark, but Lionel arrives and shoots him down. Clark manages to revive Kara and they embrace.
Back at the Kent farm, Clark and Kara remove the photo of Lara, and Kara realizes the revived memories she had were true. Kara reconsiders her image of her father but Clark assures her that Zor-El still loved her, however misguided. Kara resolves to try and find a place on Earth and apologizes to Clark for what she said.
At the manor, Lex is having a drink when Lionel comes in. Lex wonders about Lionel's recent trip to Washington and in return Lionel confirms Lex's fascination with Kara Kent. Lex denies any interest and Lionel suggests he gives up his obsession with Clark and those close to him. Lex wonders whose father Lionel really is, and says he learned how to treat Lana based on what he saw of Lionel's treatment of his wife. Lionel warns him that he's crossed a line but Lex claims he's not that person any more. Lionel warns that Lex can never fool him.
At the Daily Planet, Kara apologizes to Jimmy and thanks him for being her friend. She gives him a brief kiss that cheers him up considerably. Chloe notices and asks him to lunch as a friend, but he says he has plans and Chloe figures it's with Kara. She tries to gently warn Jimmy that Kara might be more different then he expects.
At the barn, Clark shows Lana the picture of his mother Lara then gives her the crystal, which he has hidden away in a lead box, and tells her it contains his mother's DNA.