Arrival Having been transported to the Fortress of Solitude, Clark is confronted by Jor-El, who tells him he cannot return to Smallville, instead he must stay and prepare to save the planet. Also, transported to the Fortress, Chloe is unable to handle the sub-zero temperature and collapses, begging Clark to use his powers to save her. Jor-El forbids him to leave, but finally acquiesces, telling Clark he must return before sunset or there will be dire consequences. Meanwhile, Lana is horrified when she sees two Kryptonian aliens emerge from a spaceship discovered in the remnants of the meteor shower. The two aliens destroy what's left of the town searching for Kal-El.
Mortal Jor-El strips Clark of his powers, making him human. Delighted to finally be "normal", Clark pursues a relationship with Lana sans secrets. However, after Lana, Jonathan and Martha are taken hostage by three thugs, Clark must figure out how to save his family without his super powers.
Hidden Chloe is warned by Gabriel 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 getting shot. In the hospital, Clark flatlines and his fate is left in Jor-El's hands. Meanwhile, Lex believes Lionel has the key to open the spaceship.
Aqua A summer beach party at Crater Lake takes a dramatic turn when Lois hits her head while jumping into the lake. Before Clark can save her, a mysterious swimmer, Aquaman, a.k.a. AC, comes to her rescue, out-swimming Clark and leaving him baffled. Professor Fine tells Clark that Lex is behind a covert operation manufacturing weapons. AC attempts to break into the Luthercorp Marine Center in an attempt to destroy one of Lex's torpedoes and is captured by Lex.
Thirst Lana decides to enroll at Metropolis University at the last minute and is forced to join a sorority to find housing at such a late date. However, her new sorority sisters offer her more than a place to crash after they turn her into a vampire and instruct her to kill Clark. Meanwhile, Chloe applies for an internship at the Daily Planet, but the newspaper's formidable editor may be more then she can handle.
Exposed Clark and Jonathan are thrilled when Jake Jennings, Jonathan's oldest friend, rolls into the Kent farm looking for their support in his campaign for re-election to the senate. However, after a young girl named Melissa turns up dead, it is revealed that she was a stripper and Jennings' mistress, which makes him the prime suspect. Searching for answers, Chloe convinces Lois to go undercover as a stripper, but things take a dangerous turn when Lois gets kidnapped by a diplomat's son who intends to sell her into slavery.
Splinter Clark is exposed to silver kryptonite, causing him to have paranoid delusions. 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 - but not without an agenda.
Solitude After Martha contracts a strange disease and is given hours to live, Clark turns to Professor Fine, who convinces Clark that Jor-El is the one responsible for her illness and the only way to save her is to destroy the Fortress of Solitude. However, once the two arrive at the Fortress, Professor Fine tries to free Zod and kill Clark.
Lexmas Lex is given an envelope with damaging information that will destroy Jonathan's life and must decide whether he will use it as it will also bring harm to Clark and Martha. Before he can decide what to do, Lex is shot and falls into a coma. He dreams that his mother visits him and shows him the life he could lead if he walks away from his father and LuthorCorp. In this alternate life, Lex is happily married to Lana with a baby on the way. Meanwhile, Chloe asks Clark to use his powers to deliver Christmas presents to needy kids.
Fanatic One of the volunteers on Lex's campaign staff is far too devoted to the cause, and takes matters into her own hands, hatching a scheme that even shocks Lex. Meanwhile, Martha makes a deal with Lionel.
Lockdown The two police officers who witnessed the spaceship land in the meteor shower take Lex and Lana hostage and threaten to kill them unless Lex reveals where he hid the spaceship. While escaping to the panic room in the mansion, Lex takes a bullet meant for Lana. Fearing Lex may bleed to death, Lana asks him to tell the officers the secret location, but he confesses the ship has been missing for weeks. Meanwhile, Clark discovers Lana has been researching the spaceship with Lex and fears she is close to discovering his secret.
Reckoning Clark reveals his secret to Lana, Jonathan and Lex) learn the results of the senatorial election and there is a tragic car accident on the highway that takes the life of someone Clark loves. A desperate Clark appeals to Jor-El for help.
Vengeance Clark discovers the new reporter at the Daily Planet - a bespectacled, bumbling woman named Maya - is actually a masked avenger who fights crime at night. Meanwhile, Clark's bottled-up grief threatens to get the best of him.
Tomb The spirit of a young girl is released after Lois finds a corpse in the walls of the Talon. Clark and Lois must follow the trail of the spirit and find her killer, who has been preying on girls in Smallville for the past 10 years. When Lois is suddenly kidnapped, Clark comes to the rescue.
Cyborg A sympathetic doctor releases a half-human/half-machine subject named Victor who was being held captive and experimented on by LuthorCorp. While making his escape, Victor is struck by Lana's car. After watching him walk away without a scratch, Lana calls Clark to investigate. Clark befriends Victor and promises to help him find his girlfriend, but Lex traps Victor and takes him back to LuthorCorp.
Hypnotic Lex discovers that Professor Fine, aka Brainiac is in Honduras and sets out to confront him. 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 demands that Clark kill Lex.
Void Still distraught over her break-up with Clark, Lana experiments with a dangerous serum that allows her to flat-line and see her deceased parents again. A worried Clark rushes to save Lana from hurting herself, but ends up being injected with the kryptonite-laced serum by a rogue doctor. When Clark flat-lines, he is able to talk to his father, recently deceased Jonathan), who warns him that Lionel knows his secret. Meanwhile, Lionel continues to get closer to Martha.
Fragile Clark and Martha take in a little girl, Maddie, after her foster mother is brutally stabbed to death. However, after it is discovered that Maddie has the power to shatter glass, she becomes the prime suspect. Meanwhile, Chloe walks in on Lex and Lana during an intimate moment.
Mercy A masked tormentor 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 sets out to confront him, but inadvertently becomes a pawn in the tormentors game and ends up fighting for her life.
Fade 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, Clark confronts Lana about her relationship with Lex.
Oracle Clark is stunned when he sees his father's ghost at the graveyard, but becomes even more confused after Jonathan tells him he must kill Lionel. Meanwhile, Lex develops a vaccine for Fines' deadly virus, but Fine intervenes and injects him with the vaccine, which causes a shocking reaction in Lex.
Vessel Brainiac unleashes a deadly virus, which will kill millions of people, and refuses to give Clark the vaccine unless he agrees to release General Zod. Clark turns to Lionel, who once again channels Jor-El. Meanwhile, Lex is stunned by his newfound powers and shares the discovery with Lana, who decides to stand by her new man, unaware of the shocking turn Lexs life is about to take due to Brainiac's evil machinations.