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.