Clark Kent now carries a full load of classes at Central Kansas University, but that's not all he carries. He carries the full weight of his-and perhaps the world's- destiny. From the Fortress of Solitude rising from the ice to a Metropolis in flames, this astonishing pivotal season has Clark facing rogue Kryptonians; Lex Luthor launching a vicious political campaign; Clark's love for Lana Lang deepening, while he and Lois Lane remain friendly adversaries.
Having been transported to the Fortress of Solitude, Clark (Tom Welling) 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 (Allison Mack) 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 (Kristin Kreuk) 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.
Jor-El strips Clark (Tom Welling) of his powers, making him human. Delighted to finally be "normal," Clark pursues a relationship with Lana (Kristin Kreuk) sans secrets. However, after Lana, Jonathan (John Schneider) and Martha (Annette O'Toole) are taken hostage by three thugs, Clark must figure out how to save his family without his super powers.
Chloe (Allison Mack) is warned by Gabriel (guest star Johnny Lewis) 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 (Michael Rosenbaum) believes Lionel (John Glover) has the key to open the spaceship.
A summer beach party at Crater Lake takes a dramatic turn when Lois (Erica Durance) hits her head while jumping into the lake. Before Clark (Tom Welling) can save her, a mysterious swimmer, Aquaman, a.k.a. AC (Alan Ritchson), comes to her rescue, out-swimming Clark and leaving him baffled. Professor Fine (James Marsters) tells Clark that Lex (Michael Rosenbaum) 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.
Lana (Kristin Kreuk) 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 (Tom Welling). Meanwhile, Chloe (Allison Mack) applies for an internship at the Daily Planet, but the newspaper's formidable editor (guest star Carrie Fisher) may be more then she can handle.
Clark (Tom Welling) and Jonathan (John Schneider) are thrilled when Jake Jennings (guest star Tom Wopat), 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 (guest star Sarah Mutch) turns up dead, it is revealed that she was a stripper and Jennings' mistress, which makes him the prime suspect. Searching for answers, Chloe (Allison Mack) convinces Lois (Erica Durance) to go undercover as a stripper, but things take a dangerous turn when Lois gets kidnapped by a diplomat's son (guest star Woody Jeffreys) who intends to sell her into slavery.
Clark (Tom Welling) is exposed to silver kryptonite, causing him to have paranoid delusions. The silver kryptonite makes him believe that Chloe (Allison Mack) is going to reveal his secret, Jonathan (John Schneider) is scheming against him with Lionel (John Glover) and Lex (Michael Rosenbaum) and Lana (Kristin Kreuk) are having a secret relationship. Chloe and the Kents frantically search for a cure, but it is Professor Fine (guest star James Marsters) who comes to Clark's rescue - but not without an agenda.
After Martha (Annette O'Toole) contracts a strange disease and is given hours to live, Clark (Tom Welling) turns to Professor Fine (guest star James Marsters), 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.
Lex (Michael Rosenbaum) is given an envelope with damaging information that will destroy Jonathan's (John Schneider) life and must decide whether he will use it as it will also bring harm to Clark (Tom Welling) and Martha (Annette O'Toole). Before he can decide what to do, Lex is shot and falls into a coma. He dreams that his mother (Alisen Down) visits him and shows him the life he could lead if he walks away from his father (John Glover) and LuthorCorp. In this alternate life, Lex is happily married to Lana (Kristin Kreuk) with a baby on the way. Meanwhile, Chloe (Allison Mack) asks Clark to use his powers to deliver Christmas presents to needy kids.
Jonathan (John Schneider) receives threats on his life from a mysterious source who urges him to drop out of the senate race. Later, Clark (Tom Welling) finds his dad bloody and beaten and becomes determined to find his attacker. He later discovers that a group of Lex's followers are determined to do anything to see that Lex wins the election. Lois' (Erica Durance) life is threatened when she's captured and asked to assassinate Jonathan during his speech. Lionel (John Glover) offers to give Martha (Annette O'Toole) money to help Jonathan's campaign. Lana (Kristin Kreuk) is convinced that the answers she is looking for lie in researching the first meteor shower.
The two police officers who witnessed the spaceship land in the meteor shower take Lex (Michael Rosenbaum) and Lana (Kristin Kreuk) 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 (Tom Welling) discovers Lana has been researching the spaceship with Lex and fears she is close to discovering his secret.
In the 100th episode of the series, Clark (Tom Welling) reveals his secret to Lana (Kristin Kreuk), Jonathan (John Schneider) and Lex (Michael Rosenbaum) 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.
Clark (Tom Welling) discovers the new reporter at the Daily Planet-a bespectacled, bumbling woman named Maya (Denise Quinones, former "Miss Universe")-is actually a masked avenger who fights crime at night. Meanwhile, Clark's bottled-up grief threatens to get the best of him.
The spirit of a young girl is released after Chloe (Allison Mack) finds a corpse in the walls of the Talon. Clark (Tom Welling) 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.
A sympathetic doctor releases a half-human/half-machine subject named Victor (guest star Lee Thompson Young) who was being held captive and experimented on by LuthorCorp. While making his escape, Victor is struck by Lana's (Kristin Kreuk) car. After watching him walk away without a scratch, Lana calls Clark (Tom Welling) to investigate. Clark befriends Victor and promises to help him find his girlfriend, but Lex (Michael Rosenbaum) traps Victor and takes him back to LuthorCorp.
Lex (Michael Rosenbaum) discovers that Professor Fine, aka Brainiac (guest star James Marsters) is in Honduras and sets out to confront him. Clark (Tom Welling) meets a beautiful seductress named Simone (Nichole Hiltz) 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.
Still distraught over her break-up with Clark (Tom Welling), Lana (Kristin Kreuk) 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 (Patrick Currie). When Clark flat-lines, he is able to talk to his father, recently deceased Jonathan (John Schneider), who warns him that Lionel (John Glover) knows his secret. Meanwhile, Lionel continues to get closer to Martha (Annette O'Toole).
Clark (Tom Welling) and Martha (Annette O'Toole) take in a little girl, Maddie (guest star Emily Herst), 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 (Allison Mack) walks in on Lex (Michael Rosenbaum) and Lana (Kristin Kreuk) during an intimate moment.
A masked tormentor (guest star Ian Tracey) takes Lionel (John Glover) hostage and orchestrates a series of elaborate games that Lionel must win in order to stay alive. After Clark (Tom Welling) tells Martha (Annette O'Toole) that Lionel knows his secret, she sets out to confront him, but inadvertently becomes a pawn in the tormentor's game and ends up fighting for her life.
While in Metropolis, Clark (Tom Welling) saves the life of a stranger named Graham (guest star), 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 (Michael Rosenbaum) would be the best gift he could give Clark. Meanwhile, Clark confronts Lana (Kristin Kreuk) about her relationship with Lex.
Clark (Tom Welling) is stunned when he sees his father's ghost (John Schneider) at the graveyard, but becomes even more confused after Jonathan tells him he must kill Lionel (John Glover). Meanwhile, Lex (Michael Rosenbaum) develops a vaccine for Fine's (guest star James Marsters) deadly virus, but Fine intervenes and injects him with the vaccine, which causes a shocking reaction in Lex.
Brainiac (guest star James Marsters) unleashes a deadly virus, which will kill millions of people, and refuses to give Clark (Tom Welling) the vaccine unless he agrees to release General Zod. Clark turns to Lionel (John Glover), who once again channels Jor-El. Meanwhile, Lex (Michael Rosenbaum) is stunned by his newfound powers and shares the discovery with Lana (Kristin Kreuk), who decides to stand by her new man, unaware of the shocking turn Lex's life is about to take due to Brainiac's evil machinations.