Clark confronts Bizarro, the last wraith from the Phantom Zone, and the ensuing fight causes the dam to break and a torrent of water rushes towards the land. Lex, having just been arrested for Lana's murder, is submerged under water in a patrol car, but is saved by a mysterious young woman. Lois manages to pull Chloe to safety but her cousin is pronounced dead at the hospital. The same woman who saved Lex reappears at the Kent farm and is revealed to be Kara, a.k.a. Supergirl, Clark's cousin from Krypton.
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.
Kara desperately wants to make friends and fit in on Earth, but Clark tells her to keep a low profile until she can get her powers under control. Despite his warnings, when the "Miss Sweet Corn" beauty pageant comes around, Kara signs up and meets the competition - Tyler, Carly, and Tempest - three meteor-infected vixens who plan to use their powers to steal a treasure map to the hidden Smallville time capsule.
Chloe learns that a doctor, Dr. Curtis Knox, has been treating meteor-infected people and removing their abilities. Desperate to get rid of her powers, Chloe makes an appointment to see him, unaware that Dr. Knox has a nefarious plan to kill his patients and harvest their organs. Meanwhile, Kara cons Jimmy into helping her locate her crystal and defies Clark's order to stay on the farm after she discovers its whereabouts. Lana sets up secret surveillance of Lex.
The residents of Smallville are thrilled when "Warrior Angel," a movie based on a comic book, begins shooting in town. However, after the lead actress, Rachel Davenport takes off in a stunt car with cut brakes, Clark must step in to stop the runaway car. Unfortunately, an obsessed fan witnesses this heroic event and decides Clark is a real life superhero, whose girlfriend Lana must be eliminated so Clark can fulfill his destiny. Meanwhile, Lex discovers Lionel at the cabin.
Clark learns Kara is in Washington searching for the crystal. Kara is captured after she breaks into the lab and sedated with a kryptonite-infused truth serum. The serum causes her to relive a prior trip to Earth when she followed Clark's biological mother, Lara, to the Kent farm. Clark arrives in time to save her but, after searing the machine with heat vision, he also falls victim to the serum and sees what Kara sees: his mother.
Kryptonite and high voltage mix during a lightning storm, causing Lana to absorb Clark's powers. Using her newfound super powers, she breaks into Lex's safe and steals incriminating evidence which she then delivers to Lois and Grant, demanding they run a story exposing Lex's secrets. After Grant refuses to use stolen material, Lana decides to take care of Lex herself. Clark tries to stop Lana from killing Lex and a super battle ensues between the two.
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.
Clark returns to Smallville from the Fortress and tells Lana that Kara is gone. Clark tells Lana they should team up to bring Lex down, so she gives him all the information she's gathered so far, including a report on a man named Adrian, who was infected with an alien substance. Adrian secretly plants a bomb on Chloe and tells Lois if she doesn't get Lex to admit the truth about his experiments with 33.1, he will detonate the bomb. Chloe, thinking she is about to die, confesses to Jimmy that she is a meteor freak.
While Clark is frozen in the Fortress, Bizarro takes over his life with Lana. Unaware she is with Bizarro, Lana enjoys the "new Clark" and shares information she's gathered on a serial killer who is draining his victims of all trace minerals. The two conclude it must be Brainiac and Bizarro sets off to find him. Lex is stunned at Lionel's reaction after Grant reveals he is a clone of Julian.
While secretly working for Oliver, Chloe intercepts one of Lex's project files, but she is attacked by the Black Canary, a mystery woman with a subsonic cry. Dinah Lance, Black Canary's alter ego, is a conservative talk show host who is working at the Daily Planet and clashes with Lois. Lex convinces the Black Canary that the Green Arrow and his team are terrorists so she launches an attack on the Green Arrow and Clark. Meanwhile, Lois discovers Oliver's secret.
Lois follows Lex to Detroit and discovers he has found Kara, who has amnesia. Finley, a busboy who is obsessed with Kara, fears Lex will take her away, so he shoots Lex and holds Kara and Lois captive. After Lex's comatose body is found, Chloe offers to heal him, but Clark refuses to let her.
Kara and Jimmy attend a One Republic concert and one of the roadies turns out to be former Smallville resident Pete Ross. Pete unwittingly chews some kryptonite-laced gum and develops super powers. Clark and Chloe are thrilled to meet up with their old friend but warn him against using his powers in public. However, Lex discovers Pete's powers and blackmails him into helping break into Lionel's safe by threatening to reveal Chloe is a meteor freak.
Lionel arranges to have Clark kidnapped and held in a kryptonite-lined cell at a Luthorcorp facility. After Chloe and Lana find a military electric probe at the farm, they confront Lionel, who throws suspicion onto Lex. Chloe and Lana take Kara to the Fortress and beg Jor-El to restore her memory as she is the only one who can save Clark.
Kara decides to teach Clark how to fly in order to strengthen his chances against Brainiac. However, Brainiac seems to have the upper hand against the super cousins, and some of Clark's loved ones are caught in the crossfire.
Clark desperately searches for Kara, and Brainiac is the only one who can reverse Lana's condition. Clark asks Chloe to check any large power surges in the area, so she breaks into several government computers, setting off alarms. Jimmy is caught between the Department of Security - who threatens him with jail time unless he helps them arrest Chloe - and Lex, who offers to help clear Chloe if Jimmy agrees to be in his debt.
Clark discovers that Kara sent messages from Krypton in the past that indicate that Brainiac wants to kill Baby Kal-El so Clark will not exist in the future. Clark is torn because he thinks the world would be better off if he had never arrived in Smallville. Jor-El arranges for him to see what life would have been like if Clark hadn't existed - Lex is President of the United States, Kara is raised by the Luthors, Jonathan is alive, Lana is happily married, and Chloe and Lois are ace reporters.
Lex is attacked by a cloaked stranger who carves Kryptonian symbols into his chest - a message for Clark. Chloe and Clark investigate and discover one member of the Veritas clan has survived and is hiding in a church. Clark and Lex race to be the first to find this mysterious Veritas member, who holds the key to Clark's survival.
Kara tells Lex he is destined to defeat the Traveler and offers to take him to the Fortress to learn how. Clark is stunned that Kara would go to Lex but it is revealed that Brainiac is impersonating Kara and she's actually trapped in the Phantom Zone. Chloe is arrested by the Department of Domestic Security and Lana awakens from her comatose state. Meanwhile, in an epic turn of events, Clark and Lex face off in the Fortress and Lex learns Clark's secret.