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.

Still trying to fix the aftermath of Black Thursday, Clark gets a little run down and begins to show symptoms of the common cold, including a sneeze that has some effects of its own. Meanwhile, someone kidnaps Lex.

One of the Phantom Zone escapees is up to no good in the local forest. Clark is jealous of Chloe's new boyfriend from the paper. Meanwhile, Lana and Lex finally sleep together and Lois falls in love with Oliver Queen, Martha's benefactor.

Clark and Lois are on the trail of a thief that Lois has named the Green Arrow Bandit. But this "bandit" may not be as big a villain as they believe.

Classmates from Lex and Oliver's reunion begin to die, and they begin to blame each other.

Clark is thrilled when he learns that his friend, Raya, managed to escape from the Phantom Zone and has come to see him in Smallville. The two grow close and Raya shows Clark how to restore power to the Fortress of Solitude. However, Baern, the spirit of a killer with the ability to control and feed off electricity, also has escaped from the Phantom Zone. After possessing the body of a street kid in Oakland, California, Baern makes his way to Smallville to take revenge on both Raya and Clark for his imprisonment. Meanwhile, Lana gathers more information about Lex's research project called ROCK. Also, Jimmy Olson returns to try to win back Chloe's affections by tailing Lana to find any dirt on Lex Luthor.

Lois Lane is furious at lover Oliver Queen for leaving instead of waiting till she 'makes it worthwhile' but ignores he witnessed a thug attacking a couple and was badly wounded by the carjacker he fought off. Clark reads an article about the Green Arrow striking there and drops by finding Oliver uncharacteristically careless and irritable; his X-ray vision sees Olliver injecting himself. It's a wonder drug developed for Queen Industries by Dr. Pamela Black, which almost instantly restores damaged tissue, but the scientist advices in vain against taking significant doses because lab mouse trials prove a major aggressiveness side-effect. Lex is vehemently against Lana -whose health problems are soon diagnosed a happy surprise- taking charge of fund raising for a half-way house, without telling her his reason for fearing contact with its clients, even on few occasions: he bribed Dr. Black to administer the wonder drug to its problem youths, one of which was the car-jacker. Martha Clark insists to invite Lionel for the first Thanksgiving dinner after Jonathan's death.

Lex is targeted by a former Belle Reve patient who can move through frequency, and who wants him to come clean about 33.1. Meanwhile, Clark goes to Seattle to hunt down one of the Phantom Zone escapees.

An illegal immigrant from the Mc Nally farm seeks Clark's help. He then uncovers a sinister secret in the farmer's cornfield which has been hidden since the last meteor shower.

The Daily Planet's gossip queen Linda Lake uses her ability to transform herself into water to find the dirt on people and run her weekly saucy story, however detrimental for them. After bringing out baseball star Mike Dawson is doped, Lake drags him into a fountain pond staging suicide, which fan Jimmy Olsen convinces Chloe can't be true. Next Linda overhears Chloe and Lana about her doubts to accepts Lex's marriage proposal because she is not quite over Clark and prints it, to Lex's despair and making Clark realize he's not quite over Lana either. Lex promises Linda any price to find something against Clark, and Chloe has a hard time keeping his being Kryptonian secret, while it makes her furious that people tells her their secrets while complaining when refused another's secret. When Lois tells Clark she suspects Olliver of being the Green Arrow after seeing he has an arm wound at the same spot, but wants him to be innocent either way, he finds an original way to help both friends while she gets Jimmy to help her set a trap for Ollie. Lex is prepared to wait for his pregnant lover...

The Green Arrow sends out for reinforcements and Bart Allen, a.k.a. Impulse, Arthur Curry (Aquaman) and Victor Stone (Cyborg) return to Smallville to help him take down LuthorCorp's secret lab called 'Project 33.1'. During a break-in at the LuthorCorp facility, Bart is captured and tortured by Lex for information to who hired him. Clark sets off to rescue him but is felled by kryptonite. An alarmed Chloe goes to Oliver for help, and the newly formed "justice league" springs into action to rescue Clark and Bart. Meanwhile, Oliver painfully decides to break up with Lois, feeling that his dedication to justice is more important, but he leaves out that information from her.

Clark enters a parallel environment in his subconscious where he is powerless, no one believes the truth about him, and things have turned out much, much differently.

Clark once again becomes "under the influence" of red kryptonite, and will say his true feelings on such things as Lionel and Martha's relationship, and Lana's pregnancy, but there may be someone else that will get affected by the red k.

After receiving a photo of herself dressing in her room, Lana realizes she has a stalker. After hiding out in Chloe's apartment above The Talon, Lana decides to hide out at another surprising location: the Kent farm so Lana can try to find out more about Clark as she grows more suspicious of his abilities. Meanwhile, Jimmy helps Clark try to find Lana's stalker in which he eventually breaks up with Chloe because he believes she isn't truly over Clark, forcing Chloe to take a deep look at her feelings for her best friend.

A boy who got blind during the meteor shower has developed the power to spot other meteor infected people, and Chloe is revealed to be one of them. Meanwhile, Lana closes in on Clark's secret.

Clark has second thoughts about Lana marrying Lex, Lana starts to have the same concerns. Meanwhile... the doctor involved in the secret behind Lana's pregnancy threatens Lex with his knowledge.

Clark and Chloe discover that Titan, another alien escapee from the Phantom Zone, is the hulking star of a secret fight club whose bloody, bare-knuckle battles to the death are broadcast on the Internet. Lois smells a story and investigates on her own but is captured by fight manager-presenter Maddox, the Belle Reve administrator, and forced to become wrestler Athena's first opponent. To save Lois, Clark reveals his ability to catch bullets to Maddox so he can fight Titan, but is stunned to face Lois in the ring instead... Lana returns from her honeymoon with Lex, whose men are looking for Titan, but she's more uncertain about living the life of wealthy and power and has trouble with her pregnancy.

After Lex discovers that Chloe's mother, Moira, has the power to control meteor freaks, he develops a drug to wake her from her catatonic state in the asylum, then he threatens to kill Chloe unless she uses her power to help him recover several meteor-freak escapees from his lab '33.1'. Clark helps Chloe break into the asylum to rescue Moira and finally get to know her mother, and he is almost tempted to kill Lex, but lets him live... again. Meanwhile, Clark rescues Lana from one of Lex's 33.1 escapees, and she later discovers something shocking about her "pregnancy." Also, Chloe decides to write an article about Lex's 'Project 33.1', but Lex silences her by threatening to have her locked away unless she remains quiet about his secrets projects.

After Jodi Keenan, the wife of a Special Forces soldier, sets off a pipe bomb in one of Lex's secret labs, Lionel is severely injured and Lex is taken hostage by the enraged spouse. Claiming Lex kidnapped her missing husband, Jodi threatens to blow up the entire lab with Lex inside unless he tells her where her husband is. Lex naturally denies knowing Jodi's husband, Wes, Clark sets off to rescue Lex, but is immediately felled by the kryptonite lining the earthen walls. Lex and Clark realize the only way they will make it out alive is by helping each other before the bomb detonates. Meanwhile, Lionel reveals to Lana why he forced her into marrying Lex, which leads her to investigate Lex's secret research of his 'Project 33.1' research as well as his work in tracking down the Phantom Zone escapees to capture and use one as part to create his army of 'super-human' soldiers.

After a secret meeting with Lionel, Lana is shot at the Daily Planet by a mysterious gunman. Jimmy is knocked out while studying photographs of the scene and dreams about a 1940, black-and-white version, of Smallville. Jimmy finds himself playing the role of a reporter with Chloe his secretary, and a bumbling Clark also works there, as his sidekick. Jimmy's investigation leads him to Lana, who turns out to be a very evil femme fatale who plans to orchestrate the murder of her tycoon husband Lex by using Jimmy as the patsy. Jimmy's research further takes him to a notorious nightclub owned by Lionel Luther, and Lois is a sultry singer working at club who is having a fling with Lex to help him orchestrate the murder of Lana. Meanwhile, back in 2007, Clark discovers why Lana married Lex after Chloe learns it from Lana. Also, Lois further meddles in the shooting case by stealing a silver-lined cigarette case which holds a clue.

Lex has been secretly trying to turn Wes Keenan, a military man who supposedly died fighting in Afghanistan, into a "super soldier" by injecting him with DNA pulled from the various meteor freaks he has captured. After a crooked senator, Ed Burke, who has been financing the 'Project 33.1', threatens to expose Lex's secret labs, he dispatches Wes to kill the senator. But Lois witnesses the attack and inadvertently becomes the super soldier's next target. Meanwhile, Clark tries to convince Lana to leave Lex, but she refuses and Clark becomes more suspicious about Lionel's involvement with Lana's motivation. Following Senator Burke's murder, Martha is asked to be his replacement in Washington D.C. which means leaving Smallville (and Clark) behind.

When Clark finally discovers Lionel threatened to kill him unless Lana married Lex, he goes after Lionel to silence him once and for all. Meanwhile, Lana tells Lex she is leaving him, and John Jones, the Martian Manhunter, makes a return appearance to help Clark stop Lex, who has captured the last surviving phantom escapee from the Phantom Zone, having possessed a young boy, in order to use its DNA to power him army of super soldiers at his secret lab '33.1'. Clark bids goodbye to Martha as she prepares to leave Smallville for Washington D.C., and Clark finally reveals his secret to Lana to get her to stay in town. But when Lana mysteriously 'dies' in a car bombing, Clark thinks Lex was behind it and sets off to kill him, and has a fateful meeting with the last wraith of the Phantom Zone at Lex's 'Project 33.1' lab at Reeves Dam. Lois goes to Reeves Dam in search of information about Lex's secret lab and is brutally stabbed by a security guard. Chloe finds a piratically dead Lois at the dam where in a moment of weakness, Chloe's secret power is finally revealed.