Plot

Three months after joining Jor-El, Clark crash lands back on Earth with no memory of who he is but he is found by Chloe's cousin Lois Lane who is investigating her cousin's death. Lex finds an artifact with links to Krypton in Egypt.

Three months later. Lois Lane, the second cousin of Chloe Sullivan, arrives in Smallville trying to find the missing Clark Kent to help her to find Chloe's murderer. After being struck by a mysterious ray, she loses control of her car, and finds Clark naked with amnesia in a cornfield. She brings him to Smallville Medical Center, where Martha is with Jonathan Kent, who has been in an irreversible coma. Martha brings Clark back to the farm, expecting him to retrieve his memory. However, Clark is completely dehumanized, having been taken over by his alter-ego Kal-El, whose mission is to find three Kryptonian crystals to assemble into one. Meanwhile in Paris, Lana Lang has an American boyfriend, a young man named Jason Teague, and is having a good time with him, until things take a turn when she gets hit with a mysterious spiritual force containing the spirit of a long-dead witch. Elsewhere, Lex is struggling to recover from being poisoned as he travels to bring an ancient object retrieved from an excavation in Egypt which Clark/Kal-El is also after and uses his flying abilities to steal the crystal... in midair. Also, Lois visits the imprisoned Lionel to talk with him about Chloe, while Martha has a meeting with an associate of Virgil Swan's, named Bridget Crosby, who gives her a new type of kryptonite to combat Clark/Kal-El.—Claudio Carvalho, Rio de Janeiro, Brazil

A young brunette woman is watching a video diary made by Chloe Sullivan. In the video, Chloe states that something must have happened to her and says that Clark is the only person that can learn the truth of her death. The young woman later drives to the Kent Farm, but got lost among the country roads. A lightning struck nearby and her car veers off the road into the corn field. Suddenly, a ball of light falls from the sky and a hole the shape of a pentagon is burned into the corn. In the middle lies a naked Clark Kent, who claims not to know who he is. She offers to take him to the hospital, but he instead ask her name. She introduces herself as Lois Lane.

Lois and the amnesic Clark arrive at the Smallville Medical Center, but the orderly says that she has to stay with him until he can be identified. Lois decides to stay and keep an eye on him so he doesn't wander around the waiting room naked.

In Paris, Lana is taking photographs on the street when she bumps into a young man who asks her opinion on a gift to celebrate the two month anniversary of meeting his girlfriend. After a bit of banter, it is revealed that the man is her new boyfriend, Jason Teague.

Martha Kent is reading to an unconscious Jonathan Kent when Dr. Harden informs her that she needs to think about the future and that Jonathan is brain-dead. Martha declares that she will not give up on him.

Elsewhere in the hospital, Lois starts talking to Clark about why she's in Smallville, but Clark is apathetic and keeps trying to leave. Clark wanders into the hallway and is seen by Martha, who is overjoyed to find him, but he does not recognize her. Clark tells her he is waiting for "the sign". She says that she can help him find the sign, but he must go with her immediately. Lois finds out that it is Clark, but he has already left.

Lex Luthor is in Egypt, where he obtains an ancient statue artifact. He pays a large amount of money to erase all the evidence of him visiting Egypt before leaving. Lex boards his airplane and Dr. Vaughn reminds him that he survived a massive poisoning that would have killed most people. It is also revealed that Lex must have his blood purified every 72 hours or his organs will shut down.

Martha takes Clark back to the farm and up to his loft to try and jog his memory. She shows him a picture of Jonathan and says it's his father, but Clark just replies that Jonathan is dead to him. When she realizes that his behavior is probably due to Jor-El's influence, Martha grows upset and starts to scream and cry for her son to be returned.

Lex is in his airplane returning from Egypt, when the plane hits some turbulence and the statue breaks, revealing a mysterious stone. Suddenly, Clark hears an incredibly piercing sound in his head. He says that he is "Kal-El of Krypton" and that it is time to fulfill his destiny. Martha grows upset and starts to scream and cry for her son to be returned. Kal-El says that "Clark Kent is dead", and to Martha's shock, launches himself off the ground and flies into the sky.

Lana and Jason Teague go to a church to do a tombstone rubbing of the crypt of Countess Margaret Isobel Thoreaux for an art-history class. When Lana touches a symbol on the tomb, a great surge of bright energy flows through her body. The Mark of Transference appears on her lower back.

Back at the Kent farm, Martha is trying to reach Virgil Swann over the phone. Lois arrives, having followed them home and asks Martha about Clark and Chloe's relationship. She asks about Clark, but Martha makes the excuse that Clark is sleeping to hide the fact that he is no longer there. Martha states that she will have Clark contact Lois if he remembers anything. Lois explains that she thinks Clark might know something about Chloe's death. She also states that she is trying to get in to speak to Lionel but she is having trouble getting him to accept the visit, and that Lionel would otherwise be discharged in two weeks and Chloe's murder would never be avenged. Martha warns her to stay away and tells her that getting involved with Lionel is dangerous. Lois says that she knows Martha used to work for Lionel and wants to know how she escape unscathed. Martha tells her she didn't and finally gets Lois to leave.

Meanwhile, Kal-El flies up to Lex's plane and rips off the door at 20,000 feet. As Lex and Dr. Harden are tossed about in another cabin, Kal-El steps into the plane, reaches out his hand and draws the stone through the cabin wall to him. As Lex scrambles up to look through the hole, Kal-El flies away.

Martha's request to speak with Virgil Swann is finally answered, but by his emissary, assistant Bridgette Crosby instead. She tells her that Clark flew away and Crosby realizes that he has completely embraced his Kryptonian destiny. She gives her black kryptonite, which will split Kal-El and Clark.

Lex visits his father in jail believing that he stole the Stone from him. They throw insults back and forth. Lionel tells him that he is chasing a fairy tale even though he himself has been extensively searching for the Stones by financing six expeditions over the last two years. Lex accuses him of poisoning his son and murdering Chloe. Lionel says that those responsible for him being charged for murder will feel his wrath, but claims that Chloe's death was an accident.

Kal-El goes to the Cave and activates three symbols around the octagonal hole, which opens the pathway to the inner chamber. He places the first Stone on the table. Lana somehow ended up back at her place. She hears someone banging on the door. She goes to see who it is and finds out that it's her boyfriend Jason Teague. He asks her what happened but she doesn't know how she ended up back at her apartment.

On his way out of the cave, Clark encounters Martha. When she presses the black kryptonite into his chest, Clark and Kal-El split and begin to fight each other for control. Martha throws the black kryptonite to Clark who stabs it into Kal-El, effectively combining them back, this time with Clark in control. Simultaneously, Jonathan miraculously wakes up.

Lana is taking a shower and once she steps out of the shower and wraps a towel around and looks in the mirror to see the Mark of Transference mark on her lower back.

Lois gets in to visit Lionel in jail by saying she is Martha Kent. After some back and forth, Lois tells him that she knows that safe house was no accident. As she leaves, Lois taunts Lionel with the question of whether he is being set up as he prepares to walk out of the hospital a free man.

Lois goes to Smallville Cemetery to pay her respects to Chloe, whose headstone reads "Chloe Sullivan 1987-2004 Beloved Daughter." Lois promises to find out who did this to Chloe. She is surprised when she sees Clark behind her. Clark offers to help find out what happened to Chloe and extends an invitation for Lois to stay at the Kent farm. Lois gives him some time alone at the grave and Clark X-rays Chloe's coffin and discovers it to be empty. He announces to Lois that Chloe is still alive.