| ShortSummary | - Senator Jack Jennings , Jonathan's oldest friend, arrives at the Kent farm looking for support in his campaign for re-election. When a stripper turns up dead, and is revealed to be Jennings' mistress, Jennings is made the prime suspect. Searching for answers, Chloe convinces Lois to go undercover as a stripper, but things take a dangerous turn when Lois is kidnapped by a foreign diplomat's son, who intends to sell her into slavery.
- Chloe is warned by Gabriel, a former school newspaper worker, that he is going to set off a missile and obliterate all of Smallville. Still stripped of his super powers, Clark confronts Gabriel and ends up being killed. Jor-El, in possession of Lionel's body, resurrects Clark with all his powers, but with the consequence that someone Clark loves will have to die.
- After a failed take-over of LuthorCorp, a disgruntled employee takes Lionel hostage and orchestrates a series of elaborate games that Lionel must win in order to stay alive. After Clark tells Martha that Lionel knows his secret, she inadvertently becomes a pawn in the tormentor’s game and ends up fighting for her own life.
- Lois injures herself in the lake, but before Clark can rescue her, a mysterious swimmer, Arthur "A.C." Curry, out-swims Clark and rescues her first. During his first lecture at a University, Professor Fine tells Clark that Lex is behind a covert operation manufacturing weapons. The same weapons are what brought A.C. to Smallville. Teaming up with Clark, the two destroy Lex's underwater weapon, and Clark's trust of Lex disappears completely.
- The spirit of a young girl is released from her tomb after lightning strikes a kryptonite bracelet she was wearing. Clark finds the corpse in the walls of the Talon and it attaches itself to Chloe. Clark follows the trail of the spirit to find her killer, who has been preying on girls in Smallville for the past decade. When Lois is suddenly kidnapped, Chloe has to come to her rescue.
- A sympathetic doctor releases a half-human/half-machine subject named Victor Stone being held captive and experimented on by LuthorCorp. Clark befriends Victor and promises to help him find his girlfriend, but Lex traps Victor and takes him back to LuthorCorp. Clark helps Victor free himself for good. Meanwhile, Martha is being blackmailed, and Lionel offers to step in and deal with the blackmailer. It is later revealed that Lionel knows Clark's secret.
- Jonathan's life is threatened by a mysterious source, who urges him to drop out of the race. Clark discovers that Lex's followers, primarily Samantha Drake, are determined to do anything to see that Lex wins the election. Lois is threatened into assassinating Jonathan during his senatorial speech. Lionel offers Martha some money to help Jonathan's campaign, while Lana believes that the answers she is looking for lie in the first meteor shower.
- Clark and Martha take in a little girl, Maddie, after her foster mother is brutally stabbed to death. Maddie becomes the prime suspect, at least in Lois' eyes, when it is discovered that she has the power to manipulate glass. Maddie's father arrives to claim her, and is revealed to be the real murderer. Lois takes a job as Martha's Chief of Staff, and Chloe walks in on Lex and Lana during an intimate moment.
- While in Metropolis, Clark saves the life of a stranger named Graham, who vows to repay Clark for his kindness. Unfortunately, Graham happens to be a hit man with the ability to cloak himself, and he decides killing Lex would be the best gift he could give Clark. Meanwhile, Lana tells Clark about her growing relationship with Lex.
- Two police officers, one of whom witnessed the Kryptonians land in the second meteor shower, take Lex and Lana hostage and threaten to kill them unless Lex reveals where he hid the spaceship. Lex takes a bullet meant for Lana, and fearing Lex may bleed to death, Lana asks him to tell the officers the location. Clark discovers Lana has been researching the spaceship with Lex and fears she is close to discovering his secret.
- When Martha contracts a strange disease, Clark turns to Professor Fine, who convinces Clark that Jor-El is the one responsible for her illness. Fine convinces Clark that the only way to save her is to destroy the Fortress of Solitude, separating Jor-El's link. Once the two arrive at the Fortress, Fine reveals himself to be an artificial intelligence created by Kryptonians and tries to free Zod from the [[w:c:dc:Phantom Zone
- Lana decides to enroll at Metropolis University at the last minute and is forced to join a sorority to find housing. The house leader Buffy Sanders, and her sorority sisters, offer her more than a place to crash when they turn her into a vampire. Lex provides Clark with an antidote for Lana, after LuthorCorp is revealed to be connected to the vampires. Chloe earns an internship at the Daily Planet.
- Clark is finally willing to reveal his secret to Lana, but there are consequences. Jonathan and Lex learn the results of the senatorial election and the life of someone Clark loves – Lana – is finally taken away from him. A desperate Clark appeals to Jor-El for help, only to find himself frantically trying to save her again. Lionel reveals to Jonathan he has a little more up his sleeve. Minutes later, Jonathan dies of a heart attack in front of Martha and Clark.
- Lex goes searching for Professor Fine in the jungles of Honduras. Clark meets a beautiful seductress named Simone who uses a magical charm to make people succumb to her every wish. An enchanted Clark reveals his powers to Simone, who seizes the opportunity and, after forcing Clark to break up with Lana, demands Clark kill Lex. Lana tries to reconcile her and Clark's relationship, but Clark breaks up with her thinking that they can never be together because of his secret identity.
- Fine unleashes a crippling computer virus, which will lead to the destruction of Earth via pandemonium, and refuses to stop it unless Clark agrees to release Zod. Clark turns to Jor-El, who informs him that Zod needs a vessel to inhabit. Clark must destroy that vessel, and that vessel is Lex. Lex is stunned by his newfound powers and shares the discovery with Lana, who decides to stand by her new man, unaware of Fine's true intentions.
- Chloe discovers that Professor Fine is still alive and warns Clark, who sets out looking for him. Lana, still upset over her break-up, experiments with a kryptonite drug that allows her to see her deceased parents. A worried Clark rushes to save Lana from hurting herself, but ends up being injected with the kryptonite-laced serum. When Clark flat-lines, he is able to talk to his father, who warns him that Lionel knows his secret.
- Clark is exposed to a new kind of kryptonite, causing him to have paranoid delusions about those around him. The silver kryptonite makes him believe that Chloe is going to reveal his secret, Jonathan is scheming against him with Lionel, and Lex and Lana are having a secret relationship. Chloe and the Kents frantically search for a cure, but it is Professor Fine who comes to Clark's rescue, claiming to be a Kryptonian.
- When he doesn't return, Jor-El strips Clark of his powers, making him normal. Delighted to finally be "human", Clark pursues a relationship with Lana without secrets. When Lana, Jonathan and Martha are taken hostage by three krypto-thugs, Clark must figure out how to save his family without his super powers. In the end, Clark learns that everything was orchestrated by Lex, in an effort to test Clark's abilities. Clark confronts Lex, thus ending their friendship.
- Clark is stunned when he sees his father’s ghost at the graveyard, but becomes even more confused when Jonathan tells him he must kill Lionel. Jonathan appears again, and gives Martha the same message. Lex develops a vaccine for Fine’s deadly virus, but Fine intervenes and injects him with the vaccine. Clark realizes Jonathan is really Milton Fine, and Jor-El takes possession of Lionel so that he can destroy him.
- When his mother is mugged in Metropolis, Clark decides to find out who it was that saved her life. He discovers the new reporter at the Daily Planet, a woman named Andrea Rojas, is actually a masked avenger who fights crime at night. Clark’s bottled-up grief over the loss of his father threatens to get the best of him as he joins Andrea in her fight against crime.
- Lex considers finding, or creating, damaging information against Jonathan to upset his Senatorial race, information that may harm Clark and Martha. When Lex is shot, he falls into a coma and is visited by the ghost of his mother. She shows him a life without his father, where Lex is married to Lana, and the two are expecting a second child. Interrupting Clark and Lana's first Christmas, Chloe persuades Clark to play Santa, and deliver gifts to those less fortunate.
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