Lana and Lex's relationship dissolves when she discovers the truth about her pregnancy while simultaneously discovering Clark's secret. She tries to leave Lex and Smallville with disastrous consequences. As Lex, Clark, and Lionel all search for the missing Phantom Zone escapees, Lex's Level 33.1 project advances dangerously. It becomes personal for Lois when Lex exploits one of her childhood friends and she vows to take him down. Lois and Clark have their first kiss, shadowing their future relationship. Chloe begins a relationship with Jimmy Olsen, but also discovers that she has a mysterious, latent meteor power. Martha Kent moves to Washington, D.C., to represent Kansas in the US Senate.
Clark must escape the Phantom Zone, a Kryptonian prison. Possessing Lex's body, Zod begins his plans to turn Earth into a Krypton-like planet using the alien ship's hard drive. After Lois and Martha's plane crashes near the Fortress of Solitude, Jor-El tells Martha how to kill Zod. Chloe reunites with an old flame, Jimmy Olsen.
Clark catches a cold? Sneezing manifests into a new power ~ super breath! Lois lands a job at The Inquisitor, the local tabloid. Lana moves in with Lex. Lex is abducted after displaying superhuman powers in the public eye. And there's a new visitor in Metropolis called Oliver Queen.
Lex throws a charity ball. Meanwhile, Clark and Chloe pursue a Zoner who uses male human bodies as potting mix to procreate. The stakes just get higher when Jimmy Olsen gets all tied up by the Plant Lover, while love interests intesify between Oliver and Lois, and Lana and Lex.
Clark encounters Baern, a Phantom Zone escapee who absorbs various sources of energy to power radioactive strength. Tag-teaming with Raya, Clark realizes that he must fulfill his destiny. Meanwhile, Lex and Lana's relationship entangle deceit and double standards.
Clark discovers that his neighbor, Jed McNally, is holding migrant laborers captive and forcing them to work on his farm. Feeling guilty since he sees himself as the ultimate illegal immigrant, Clark seeks help from Martha to allow a young boy and his mother to stay in the country.
Daily Planet gossip columnist Linda Lake has the ability to turn herself into water and uses it to secretly overhear conversations for her column. Meanwhile, Lois begins to suspect Oliver is the Green Arrow and enlists Clark's help to prove it.
The beginings of the Justice League forms, including Impulse, Aquaman, Cyborg, and led by the Green Arrow. Clark discovers what team work really is as the Justice League blows the lid off Project 33.1.
Clark wakes up in a mental asylum where Dr. Hudson tells him he has been there for five years due to his elaborate fantasy that he has alien superpowers. In this new world, Martha Kent is married to Lionel Luthor, Chloe is deemed insane, and Lana chose Clark over Lex.
Lois tries on lipstick made with red kryptonite and becomes overwhelmed with desire for Clark. The two share a kiss and his inhibitions immediately shut down. Fueled by the red rock, Kal crashes Lex and Lana's engagement dinner and kidnaps the bride-to-be.
Clark and Chloe discover Titan, a Zoner, is the star of a secret fight club whose bloody battles to the death are broadcast on the internet. Lois investigates but is captured and forced to participate. Clark reveals his powers so he can fight Titan and save Lois.
Lex develops a drug to wake Chloe's mother Moira from her catatonic state and forces her to control meteor freaks by threatening to kill Chloe. Clark helps Chloe break into the asylum to rescue Moira and finally get to know her mother.
Jodi Keenan kidnaps Lex and injures Lionel to find out the truth about the death of her husband Wes. They become trapped in collapsing tunnels and 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.
Lana is shot at the Daily Planet by a mysterious gunman. Jimmy passes out while studying photographs of the scene and dreams about a 1940s version of Smallville in which Lana is a femme fatale who orchestrated the murder of her tycoon husband Lex and Clark works at the Daily Planet as a reporter. Meanwhile, back in 2007, Chloe discovers why Lana married Lex.
Lois's investigates a senator named Burke, who is attempting to shut down one of Lex's projects. After Burke is murdered, Lois learns that Lex is using her childhood friend Wes as the project main prototype.
When Clark discovers Lionel threatened Lana to marry Lex, he goes after Lionel to silence him once and for all. Lana tells Lex she is leaving him, and Martian Manhunter makes a return appearance to help Clark stop Lex, who is trying to find the last wraith in order to use its DNA to power his army of super-soldiers. Meanwhile, Lois goes to Reeves Dam in search of information about Lex's secret lab and is brutally stabbed by a security guard. Chloe's secret power is revealed.
The inside of the Phantom Zone is seen for the first time while several other aliens are released from it. The ongoing plot throughout the season is for Clark to recapture the escaped prisoners from the Phantom Zone.
John Glover is promoted to Annette O'Toole's 'with' billing as she is promoted to the show's first 'and' billing.