Sarkissian and a bald man attack the house, capturing Sarah and John. Cameron's chip is compromised due to the explosion, and she begins to follow orders to terminate John. Sarah and John escapes from the house, seeking refuge in a church, where they set up a trap to short-circuit Cameron in order to remove her chip, but fails due to a unfit screwdriver; they run again. John hides in a garage, but exposing his location when trying to hot-wire a truck. Before Cameron can approach him, Sarah arrives in another truck, hitting and immobilizing Cameron, enabling John to deactivate her. When Cameron's endoskeleton is about to be destroyed, John is at odds with his mother, deciding to reactivate her, and Cameron is repaired. The buyer of the Turk turns out to be a T-1001 Terminator posing as the CEO of a high-tech company.

Lex finds a amnesiac Kara in a restaurant in Detroit, and convinces her to go with him. The busboy obsessed with Kara is unwilling to let her go; he locks her in a cage, putting a bullet in Lex's head, imprisoned Lois who follows Lex. At the Smallville medical center, Lex is in a coma. To get Kara's whereabouts, Clark risks his life to enter Lex's mind with the help of a Luthor Corp machine. When Lex is about to die, Chloe uses her healing power to resurrect him, but this time the side effect is more serious than the first time. Clark finds a good side of Lex in his mind before rushing to Detroit, saving Kara and Lois.

While working for Oliver to intercept Lex's confidential information, Chloe is attacked by Black Canary, who is dedicated to seek justice with her subsonic power.

After finding that Green Arrow is behind the attacks on his falicities, Lex pays Black Canary to get rid of him. During Canary's attack at Oliver's place, Lois discovers that Oliver is the Green Arrow.Clark manages to convince Canary that Lex is the villian, and Canary accepts a spot offered by Oliver on his team.

Michael confronts Self about Scylla, and Self denies knowing it consists of six pieces, threatening to put them in prison if they don't find out the other cardholders.

Self talks to his superior, who is determined to have the mission canceled after learning the recent situation.

Michael deciphers an e-mail which contains partial information about the next meeting of the cardholders, and they have to infiltrate a main server in Anaheim to get the other two e-mails.

While trying to decipher them, Michael realizes that Self has started to shut down on them. To block the signal Sell uses to chase them, they run into a tunnel, where Michael uncovers the location of the meeting before they hijack a taxi, heading there. At a Power Plant, all of them are captured except for Michael, who manages to record the cardholder's meeting with his cellphone before presenting it to Self. The gang are given an another chance and sent back to the warehouse.

In Chicago, Bruce is tied to a chair, tortured by Wyatt, who kills him after get the information on Michael's whereabouts.

T-Bag, disguised as Pfeiffer, calls the Gate company and finds out that Pfeiffer is supposed to be the best salesman in the U.S.

With Lana's help, Bizarro tracks down Milton Fine in hope that Fine can shed light on how to prevent him from being afraid of the yellow sun. Clark is released by Jor-El to defeat Bizarro, and he pays a visit to a kryptonian scientist to seek blue Kryptonite which can make Bizarro explode. Holding the blue Kryptonite, Clark confronts Bizarro, but unable to defeat him, dropping the stone. Lana grabs it, destroying Bizarro before taking stock of the days living with him. Fine approaches the scientist, who is the creator of him, to find a way to cure himself. Lex hires an assassin to kill Grant after Grant told Lionel the truth.

A bomb is put in Chloe's purse by Adrian, a failed clone escaped from Lex's lab, and he threatens to detonate the bomb if Lois doesn't expose Lex's experiment. Grant realizes that he is a clone of Lex's brother Julian after Lex is confronted by Adrian. As a punishment, Clark is confined in the Fortress, and Bizarro leaps at the opportunity to pose as Clark and team up Lana to bring down Lex.

Clark releases Lara from the crystal in defiance of Jor-El's warning, unbeknown to him, Zor-El is resurrected, too. To protected Lara, Clark takes her to Oliver's house. Before heading to fight Zor-El, he receives a blue ring which deprives him of his power immediately. Meanwhile, Zor-El tricks Kara to tell him Lara's whereabouts; he forces Lara to be with him after defeat Clark.

In order to stop Zor-El from destroying the world, Clark shatters the crystal, destroying Zor-El along with Lara before learning Kara is missing. In Detroit,Kara wakes up in the middle of a street, suffering from amnesia.

Grant is revealed to be Lex's little brother Julian.

Lana and Clark are struck by lightning, which causes Lana to have Clark's abilities. She becomes aggressive and uses the power to torment Lex. 

As usual, the ending is quite predictable; Lana is deprived of her ability by Clark, who saves Lex along the way.

Meanwhile, Fine's remains is released from one of Lex's facility.

In search of the crystal, Kara flies to Washington, breaking into a laboratory where the crystal is allegedly kept, but it is to no avail.

Following a lead, Kara rushes to Lex's mansion, where she is ambushed and captured by Agent Carter after he uses a pair of Kriptonite handcuffs to deprive her of her ability. In a laboratory, Carter attempts to access Kara's memories, and it is turn out that she has come to the Earth before. In the nick of time, Clark comes to her rescue, seeing his mother, Lara, through Kara's memories. In the end, it reveals the crystal is obtained by Clark.

T-Bag is struggling in the desert with Sancho, his Mexican companion, suffering from dehydration and starvation. After accidentally killing Sancho who tries to attack him, T-Bag, desperate to survive, turns himself into a cannibal. He hitchhikes to San Diego, where he uses the bird book to retrieve Whistler's fake passport before heading to L.A..

Michael's team settles in a warehouse, where a new partner, Roland, versed in electronics, joins the team.  With Noland's help, Mahone recognizes Tuxhorn's driver from military database. They follow him to a heavily secured house riddled with surveillance cameras, and realize the difficulties they are facing are more than extraordinary.

Roland introduces his device which can absorb electronic data within ten feet. Assuming that Tuxhorn would bring Scylla with him, Michael dispatch Sucre and Bellick to wreck Tuxhorn's car, so they can get close to him and copy the data, but it turns out to be a dead end.

Sara surruptitiously slips the device into Tuxhorn's maid's purse and Roland successfully receives signals emitted from Scylla. But when Bellick grabs the purse from the maid, the team is frustrated to find that the device is gone.

With the distraction made by Sucre and Lincoln, Michael and Mahone break into the house, retrieving the device. While downloading the data from the device, Roland discovers that Scylla has six pieces, and they just got one of them.