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.

A Warrior Angel film is being shot in Smallville, where the lead actress is saved by Clark from a car crash. After witnessing Clark catching a bullet, Ben, a fan of the comic book, makes it his obligation to kill Lana in order to prompt Clark to fulfill his destiny.

Lionel is confined in a secluded cabin, and Lana is the mastermind of the kidnapping.

To avenge Sara's death, Michael follows Gretchen to Los Angeles, planning to kill her while she and Whistler are on a mission to retrieve a card containing crucial information about the Company. 

Held at gunpoint, She confesses that Sara had escaped and the head was a fake. 

Unaware that Whistler has made a copy of the card, Gretchen goes to meet the General, who is intolerable of her fault and orders Waytt to kill her.

Mahone and Whistler are now working together against the Company; they try to enlist Michael's help, by promising to reveal Sara's whereabouts. But Whistler is shot in the head by Waytt when trying to convince Michael in an alley. 

In Panama, Lincoln kills a man sent by the Company before surrendering to the police to protect L.J. and Sofia. Bellick and Sucre escape from Sona after a riot takes place and is smuggled back in the U.S., where they are apprehended by the police while Sucre is visiting his baby daughter. 

T-Bag also escapes and resolves to revenge himself on Michael; on his way back to America, the smugglers rob him, taking his money, leaving him in a desert. After talking to his wife on the phone, Mahone joyfully heads home to reunite with his family; much to his grief, he arrives at home only to find them brutally murdered.

In Chicago, Michael contacts Bruce, a trusted friend of Sara's father, in the hope that he can shed light on Sara's situation, but is arrested before he can get any information. He is approached by Agent Donald Self, a Homeland Security official dedicated to bring down the Company, and requested to infiltrate a Company facility to decrypt the card, in exchange for his freedom. Before he can respond, Bruce bails him out, driving him to a secluded house where Sara is waiting for him; they embrace.

At night, Waytt tries to assassinate them, but fails, prompting Michael to accept Self's offer.A team consists of Michael, Lincoln, Sucre, Mahone, Bellick and Sara board a plane to start their mission, and they will all be free once the mission is accomplished.

The Martian Manhunter barges into Clark's house, warning him not to trust Kara, saying her father had tried to assassinate Jor-EI.

Eager to be normal again, Chloe leaps at the chance to undergo a procedure which will rid her of meteor rock toxins, unaware of the operator, Dr. Curtis Knox's malicious intention to transplant her heart to his love. Of course, Clark will never let that happen :]

Lana spends the $10 million stolen from Lex to bribe his security guard to spy on him.

Kara participates in a beauty contest over the objection of Clark, who worries that she would expose her ability.
Lana returns to Smallville, astonishing Clark, with Lex living up with his promise to drop the legal charge against her, she finally reunite with Clark.
In the end, Kara is confronted by Lex, who vows to unravel the mystery of the Kents after she denies having saved him.

Clark's cousin, Kara, was sent to earth after him, but her ship was stuck under Reeves Dam. With the dam demolished, she is finally released, but finds out that her ship is stolen. Having reunited with Clark, she finds her ship and stops it from exploding, but the crystal in the ship has gone. Lana is confronted by Lex, who apologizes to her before revealing her scheme to fake her own death by using a clone of herself.

Clark decides to finish his training; at the fortress, he tells Jor-EI about Kara, but Jor-EI warns him not to trust her.

The fighting between Clark and Bizarro causes Reeves Dam to burst. Clark uses his heat vision to vaporize the flood, saving a boy and his father. Trapping in a police car underwater, Lex is saved by a mysterious woman he believes to be an angel.
Pronounced dead by the doctor, Chloe miraculously resuscitates herself in the morgue. With the Martian Manhunter's help, Clark defeats Bizarro. Lana is alive, seen in Shanghai, China.