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 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.