John Jones, the martian-like creature that helped Clark defeat two Phantom Zone prisoners, visits a small Quebec village where an elderly man is apparently possessed by a demon. Jones knows that it isn’t a demon that has inhabited this man, but the final Phantom Zone prisoner. Jones’ attempt to drive the prisoner out fails when the wraith wounds him. Moments later, Lex arrives in the village with his Project Ares team leader, Bartlett, and a small army. Lex wants the elderly man taken alive so his team can harvest the alien peptides from the wraith inside him for Lex’s army of super soldiers. The wraith manages to evade Lex by leaving the elderly man’s body. Intent on getting the peptides at all costs, Lex orders Bartlett and his men to search the area until they can capture whoever the wraith inhabits next.
After returning to his mansion in Smallville, Lex is confronted by his father. After informing his father that he knows Lana has been working with him to uncover the secrets of Project Ares, Lex learns from his father the true reason Lana married him. A furious Lex wants nothing to do with Lionel, but Lionel reminds his son that he won’t be so easy to get rid of. Meanwhile, Clark bids Martha farewell. Before Martha leaves Smallville, she tells Clark that now might be a good time for him to consider moving on. Later, Lana informs Clark that she is leaving Lex and Smallville for her own safety. Clark tries to persuade her not to go by letting her know about his alien heritage. Though Lana knows that Clark could protect her, she still wants to leave for Clark’s own good, fearful that Lionel may act on his promise to kill Clark if she leaves Lex. Before she prepares to leave town, Lana tells Clark about Lionel’s promise.
Clark storms into LuthorCorp and attacks Lionel. Lionel tries to explain that his threat wasn’t genuine, but only made so Lana would marry Lex and be close enough to him to learn more about Project Ares and how the final wraith from the Phantom Zone fit in. Clark refuses to believe Lionel. Just as he’s about to injure Lionel, John prevents that from happening, claiming that everything Lionel has told Clark is the truth. Like John, Lionel is an emissary of Jor’El that was given all of Jor’El’s knowledge through a series of symbols that decipher out the kryptonian symbol for power. Meanwhile, Lana tells Lex that she knows he faked her pregnancy and is leaving him. Lex blames Clark for her decision and calls him the biggest liar of them all. After Lana tells Lex that Clark will always mean more to her than him, Lex strikes her across the face.
John informs Clark that he worked as a bounty hunter for Jor’El when he was alive, and promised to look after his son for him. He was only to reveal himself to Clark after Clark passed Jor’El’s test, but the release of the Phantom Zone prisoners forced him to reveal himself sooner. Clark tells John and Lionel that he will go after the final wraith by himself, using the crystal that Raya gave him to trap it. John and Lionel are certain that Raya’s crystal won’t be of any help, as this wraith is not just any normal alien, but the product of an experiment gone wrong in a Kryptonian laboratory. It has been jumping from body to body until it finds a kryptonian’s body to host it. If Clark fails to defeat it, it could destroy him.
Even though Chloe has warned Lois against going after Lex, Lois is intent on getting a measure of revenge on Lex for his part in her friend Wes Keenan’s death. Lois breaks into Lex’s Project Ares laboratory under Reeves Dam, but is stabbed by a security guard during a scuffle. Just before she passes out, Lois places a desperate cellphone call for help to Chloe. Elsewhere, Lionel watches on in horror as Lana gets into her truck and it explodes. Later, Lionel is forced to share the heartbreaking news of Lana’s death with Clark. Convinced that it was Lex who planted the bomb in Lana’s truck, Clark swears he will kill Lex. Lionel pleads with Clark not to make a mistake he will regret by committing cold blooded murder. Clark doesn’t care. He decides to go after Lex, forcing Lionel to go after Clark to stop him.
Chloe answers Lois’ distress signal, leading her to the laboratory under Reeves Dam. Chloe finds Lois’ dead body sprawled out on the floor. As Chloe cradles her cousin in her arms, tears flow freely from Chloe’s eyes. One hits Lois’ face, bringing her back to life. Chloe’s meteor power is revealed. Unfortunately, Chloe’s usage of her power leaves her in an unconscious state. Elsewhere in the laboratory, Lex’s team are doing experiments on Phillipe Lamont, a boy from the Quebec village that the wraith has inhabited. The head doctor on the Project Ares team takes a sample of Phillipe's DNA and learns that it contains the peptide sequence that Lex needs to bring more super soldiers to life. Lex makes a desperate flee, leaving Bartlett and the doctor for dead when Phillipe manages to free himself from his restraints.
In the end, Clark confronts Lex at the Reeves Dam laboratory. Lex is shocked to find out that Lana is dead. Before Clark can react, the wraith appears. Lex flees for his life, leaving Clark alone to deal with the wraith. The wraith manages to take some of Clark’s DNA, turning it into an evil version of Clark called Bizarro. An epic battle ensues between the two. Lionel shows up in the midst of the battle, mistaking Bizarro for Clark. When Clark informs Lionel that Bizarro is not him, Lionel tries to help Clark by exposing Bizarro to kryptonite that he intended to use on Clark if he had no other way to stop him from killing Lex. Instead of having the same weakening effect it has on Clark, the kryptonite makes Bizarro stronger. Outside the laboratory, Lex is surrounded by a small army of Smallville police officers. They arrest him for the murder of his wife. Back inside the laboratory, Bizarro knocks Lionel out. He then resumes his fight with Clark, which ends with Clark being knocked into the depths of Reeves Dam. Bizarro proceeds to fly off, the skin on his face becoming chalky and cracked.
Starring: Tom Welling (Clark Kent), Kristin Kreuk (Lana Luthor), Michael Rosenbaum (Lex Luthor), Erica Durance (Lois Lane), Allison Mack (Chloe Sullivan), John Glover (Lionel Luthor), Annette O'Toole (Martha Kent)
Guest Starring: Phil Morris (John Jones), Gerard Plunkett (Dr. Donovan Jamison), Ben Ayres (Bartlett), Mylene Dinh-Robic (Young Woman), John Hainsworth (Elderly Man), Quinn Lord (Phillipe Lamont), Heather Doerksen (Chofer), Clint Carleton (Security Guard), Tyler McClendon (Deputy), Patrick Keating (Priest)
Written by Todd Slavkin & Darren Swimmer
Directed by James Marshall