As Clark and Lana get more romantically close to each other, the comatose Dr. Fredrick Walden recovers and repeats the sentence "the day is coming, and he will rule the world" many times. He believes that Clark Kent is a menace to mankind. He escapes from the mental institution using a strong power he has achieved and tries to eliminate Clark. Meanwhile, Dr. Helen Bryce returns to Smallville for her engagement party with Lex Luthor, and finds her office broke in and the blood sample of Clark Kent stolen. But who took the blood sample and her office files? Lionel or Lex? Clark is asked by Lex to be the best best man, and Martha and Jonathan Kent to replace his missing parents, as Clark begins hearing voices coming from his spaceship. Also, the evil Lionel Luthor continues playing mind games by trying to poison the relationship of Helen and Lex, as well as Chloe and Clark by offering her an intern job in Metropolis in exchange for her to investigate Clark. But unfortunately, Lionel overhears the revelations of Dr. Walden to Lex about Clark being an alien.

As Clark has finally begun dating Lana, Helen Bryce cancels her wedding to Lex after being told to by Lionel. But later, Helen realizes that she loves Lex and they finally get married. Meanwhile, Jonathan and Martha are thrilled to learn Martha is pregnant. The memory/spirit of Jor-El speaks to Clark via the spaceship, telling him he must leave Smallville, his parents and friends to fulfill his destiny. Clark decides to destroy the spacecraft, and the spirit of Jor-El with it, by using Lionel's kryptonite-made hexagon key that he made a copy of off the late Dr. Walden, in order to use it on the cave wall to learn the kryptonian markings. Clark, with Pete's help, steals the key and uses it to activate the spaceship, knowing the kryptonian radiation will destroy the ship. The ship does explode, but the shock wave injures Jonathan and Martha, causing her to miscarry. Chloe, jealous of Clark and Lana's blossoming romance, accepts Lionel's proposal to investigate Clark and gets the job at the Daily Planet. Clark, grief-stricken at the injury he caused his mother, puts on the red kryptonite ring and heads out of town on a motorcycle, planning never to return. Elsewhere, Lex, flying off on his honeymoon, wakes up alone on the airplane that is about to crash in the ocean...

Metropolis, three months later. Clark Kent (under the influence of the red kryptonite ring) has becomes a criminal, heisting banks, going to night-clubs, and living under the alias 'Kal'. But he comes into conflict with not only his Kryptonian-marked chest, but a ruthless and greedy gangster, named Morgan Edge, who wants an ever increasing percentage of the stolen loot, and also begins to suspect Clark's alien origins. Meanwhile, Lex Luthor is declared dead, but he is living with the weird Louis Leery Jr. in an isolated desert island. Back in Smallville, Dr. Helen Bryce comes to his funeral and meets Lionel Luthor in the mansion where secrets are disclosed. Lana Lang and Jonathan Kent try to bring Clark back to Smalville. Unsucessful after Lana's pleas to Clark, Jonathan makes contact in the cave with the spirit of Jor-El who imbues Jonathan with Kryptonian super-powers to combat Clark and bring him home... in exchange for a price. Also, Chloe enjoys her new job at the Daily Planet, while tailing Lana during her search for Clark.

Lex believes that he needs his memories back,but Clark can't take the risk of his secret being exposed.

At the Kent farm, Clark Kent is surprised in the middle of the night by a naked young woman claiming that she is Kara from Krypton, and asking him to go with her somewhere through the Kawatche caves to be "re-born" with the spirit of Jor-El. Kara also forces Jonathan to reveal the secret deal he made with Jor-El at the beginning of the season. Meanwhile, Clark decides to testify against Lionel to keep him in prison. Lionel sends a key of the secret chamber in the Luthor Mansion to Clark where he finally discovers the reason for the last three years of Lex's personal investigation of him, and he ends his friendship with Lex. Agent Loder continues investigating Clark's origins, until Kara finds him eavesdropping on the Kents and she eliminates Loder for good. Also, Lana leaves for Paris and Chloe and her father are included in the witness protection program. Events come full circle as Jonathan unsuccessfully tries to stop Clark from traveling through a dimensional gateway in the cave wall, Martha observes a Kryoptonia symbol that appears in a open field, Lex is alone in the mansion when he had a drink of brandy which is poisoned, Chloe and her father arrive at a FBI safe house... which explodes with them still inside, and Lionel accepts his new look in prison, but satisfied knowing that his revenge against all those involved with his incarceration has been accomplished.

The Kryoptonian metallic disc is returned to Clark following the death of Virgil Swann. Placing the disc in the cave reveals a message from the spirit of Jor-El instructing Clark to find the three Kryptonian knowledge crystals and unite them before others find them and use them to self-interest. The message goes on to tell Clark that allowing a human to assemble the crystals could lead to the destruction of Earth. The first stone, retrieved by Lex in Egypt in the season opener, is in Clark's possession in the cave. The second is apparently in possession of the late Swann's associates. And the third is located somewhere in China. Clark joins forces with Lana where they venture to China to search for the stone where Lex and Jason are also on the hunt for the stone. But they end up captured by the Chinese authorities and tortured for information to the stone's location, and it leads to the spirit of Isobel once again commandeering Lana's body to fight everyone to take the stone for herself.

When Lana (possessed by Isobel) kills Genevieve Teague by stabbing her with one of the Kryptonian Knowledge Crystals after she attempts to steal it, it triggers a cosmic event that not only severs Lana's link to the spirit Isobel but also sends meteorites from deep space toward Earth and Smallville. At the graduation ceremony for Smallville High, the military arrives to evacuate the town after news that another meteor shower is imminent. Fearing he has a link to the meteorites, Clark goes to talk to the spirit of Jor-El, who informs him that his only hope is to unite the knowledge crystals in the cave. With time running out, Clark sets about locating the final two crystals as meteorites reign down upon Smallville. Lana gives Clark the third stone they recovered from China, which was in her possession all this time, while the second stone is on Lionel's person, which activates. Lex offers to protect Lana and have her flown to New York City, but she gets caught in the meteor shower while riding in a helicopter. Lois manages to get out of Smallville in time, but Chloe stays behind to follow Clark who retrieves the final one from Lionel which hits them with a burst of energy driving him comatose. Chloe helps Clark retrieve the final stone from the Luthor mansion safe after he is immobilized by kryptonite, and helps him escape from Lex. Clark manages to unite all three stones, which transports him to the wild tundra of the frigid North Pole...

A meteor shower bursts from the heavens, raining destruction on the unsuspecting citizens of Smallville, Kansas.

While returning home with Lois, Martha is hit by a flash of light followed by a thunder and contracts a lethal Kryptonian disease. Clark fears that Jor-El thus makes him pay for his resuscitation and asks for help from Professor Milton Fine, who tells Clark that Jor-El was a dictator on Krypton, who destroyed their great leader General Zod and the planet but sent Clark to Earth to dominate the world; the death of Martha would only be prevented by destroying the Fortress of Solitude. Meanwhile, Lionel convinces Chloe to investigate who Milton Fine really is. When Lois, feeling offended because Lex called her a "muffin peddler", meets Chloe, the double visits LuthorCorp., where the truth is revealed: Professor Milton Fine is actually a Kryptonian artificial intelligence unit, created by Jor-El but re-programed and corrupted by the Kryptonian rebel General Zod, who was executed for treason, and had his spirit banished to the hell-dimension of the Phantom Zone. Fine, a Brain-Interactive-Construct (aka: Brainiac), is trying to trick Clark into releasing Zod's spirit from the Phantom Zone by destroying the Fortress of Solitude.

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, forcing Clark to appeal to Jor-El for help.

After "being prepared" by Fine, Lex is abducted in a field by a strange light. Meanwhile, Clark goes to the Fortress of Solidude where the spirit of Jor-el gives a dagger to Clark and advises him to destroy Lex, who would be the vessel of the spirit of Zod outside the Phantom Zone in which Fine, the Brain-Interactive-Construct, is trying to release. Martha travels with Lois to Washington in an airplane of the Luthorcorp. When Zod is released, he possesses Lex, and traps Clark in the Phantom Zone. Fine unleashes a powerful computer virus, creating chaos on Earth. Lois and Martha faint in the airplane without oxygen as another copy of Fine/Brainiac hijacks the plane. Chloe and Lionel are attacked by a raged crowd, while Lex/Zod and Lana declare their love for one another as both plan to travel their path together on the dark side...

With Clark banished to the Phantom Zone, Metropolis is in shambles as the city riots, and Chloe & Lionel plot to rid Lex of General Zod...one way or another.

Clark and Lois discover Kara's spaceship but before they can open it, Kara appears and knocks Lois out. Clark is shocked after Kara tells him she is there to protect baby Kal-El. Despite Kara's appearance, a despondent Clark decides that without Lana there is nothing keeping him in Smallville, and heads to the Fortress of Solitude to begin his training as a superhero. However, Jor-El tells him Kara's father- Zor-El, who is Jor-El's brother- is evil and Kara is dangerous, therefore Clark must stay in Smallville to find out why she came to Earth. Lex makes a stunning discovery regarding Lana and Project 33.1.

Clark hears the voice of his biological mother, Lara, calling for help from Kara's crystal and decides to release her, despite Jor-El's warnings. Lara and Clark reunite and she gives him Jor-El's ring, which contains blue kryptonite. As Clark puts it on, he realizes Zor-El manipulated the whole thing and that blue kryptonite strips him of his powers, enabling Zor-El to take control of the Fortress of Solitude. Meanwhile, Chloe and Lex each discover Lois and Grant have been seeing each other and warn them to stop.

While Clark is still frozen in the fortress, Bizarro grows closer to Lana, who returns the feelings on just as deep a level, even sharing some badly-needed information with him while he still attempts to carry out his intentions of destroying Clark. Lex's brother, Julian, reveals himself to Lionel in an effort to clear the air between all parties involved.

Clark is shown by Jor-El what life on Earth would have been like, had he not sent him there instead of facing the doom of his fellow Kryptonians.

When Chloe begins having memory loss when the essence of Brainiac begins replacing her memories with Kryptonian codes, Clark decides to use the Crystal of Knowledge to reconstruct the Fortress of Solitude and ask the spirit of Jor-El for help. Meanwhile, Jimmy begins to worry about Chloe's well-being, while Davis, disturbed by the knowledge that he may have alien origins, begins to become drawn to Chloe.

Clark decides that he is ready to start his training at the Fortress of Solitude to become 'Superman'. However, the spirit of Jor-El insists that he return to Metropolis to cut his ties with the people he knows before he begins. Lois reappears in the city with no recollection of vanishing to the future. Her investigation into a monorail crash brings her into contact with a new reporter named John Corben. John is opposed to the "Red and Blue Blur", and has a secret power and identity himself. Meanwhile, Chloe's friendship with Clark deteriorates when he refuses to use the Legion ring to go back in time to save Jimmy. Elsewhere, Oliver turns down a dark path in his quest to rid the world of evil. General Zod makes his entrance at the Luthor mansion before Tess.

After an accident, Clark (Tom Welling) is able to read Lois' mind, then he asks her out. Meanwhile, a washed up Oliver finds himself in danger.

Oliver is tortured incessantly by Rick Flag until Chloe, who used the Dr. Fate's helmet to find him, exchanges herself for him. Awakening in a secret LuthorCorp lab among partial Lex clones, Tess meets young Alexander before the bloodthirsty, dying senior knocks her down and uses Lois, who enabled Clark's healing by removing the fatal blue kryptonite, to set a sadistic trap. Despite his success, Clark lets his confidence be undermined by Jor-El in the ice fortress, but reconsiders after a pep-talk from Jonathan.

Clark Kent is in nostalgic mood after Martha signs over the deed to the farm as a wedding present, wondering whether it suggests he and Lois should sell and move. Clark Luthor surprises him, using the mirror box and shattering it after having sent Kent to his world, then fool everyone for a while, in search of bloody vengeance on at least one Luthor. Kent finds himself, public enemy number one against whom everyone caries green kryptonite, at Oliver's funeral, where a bitter Jonathan scolds the 'scrooge'. Recognized and helped by the other Lois, he seeks to appease hatred and find a way back. Dr. Emil Hamilton frantically tries to repair the mirror-box, just in time.

Searching for the Bow of Orion, the only known means to stop the Darkness, Oliver and Kara independently reached the same booby-trapped underground sanctuary. Kara got herself trapped, but Oliver rescues her in Indiana Jones style. Together they decipher and follow the clues to the bow, only to be get a bitter surprise. Meanwhile instead of giving his blessing in the fortress, Jor-El temporarily transfers Clark's super-powers to his already far too cocky bride.

The story of Clark Kent culminates in this two-hour series finale as Clark takes the last step to becoming the Man of Steel.