A sense of foreboding surrounds Smallville as Clark must choose between staying with Lana and his family or fulfilling his destiny to rule the Earth. Lex and Helen prepare for their marriage, and Chloe considers Lionel's offer to investigate Clark.

Under the influence of red kryptonite, Clark is following a life of crime in Metropolis while his friends and parents desperately try to find him. Lex is forced to confront his personal demons on a desert island, while Lionel holds a funeral for his presumed-dead son. And Jonathan Kent must pay a high price for the power necessary to bring his son back home.

Believing that key information about his father's past was lost when his memory was erased, Lex decides to join an experimental program with Dr. Garner to regain the information so he can turn his father over to the FBI. Knowing that Lex will discover his secret if he regains his memory, Clark tries to stop him but is caught by Lionel and the doctor and exposed to the same radical treatment so that Lionel can solve the mystery of Clark's past.

After Clark receives a message from the recently-deceased Dr. Swann, he and Lana follow Jason and Lex to China in search of one of the kryptonian crystals. Lana is tortured, causing Isabelle to emerge and wreck havoc in her search for the crystal.

After a nightmare, Clark goes to the cave to confront his father Jor-El. Jor-El warns that the crystals have fallen into human hands and have triggered a new meteor shower which will annihilate the Earth unless he reunites the three crystals. Meanwhile, Lex helps Lana, who has apparently commited murder, but then turns against her to get possession of her Kryptonian stone. As disaster looms, Chloe and Lois try to find Lana while Clark attempts to reassemble the stones, and Jason returns to make things unpleasant for the Kents.

Having been transported to the Fortress of Solitude, Clark is confronted by Jor-El, who tells him he cannot return to Smallville, instead he must stay and prepare to save the planet. Also, transported to the Fortress, Chloe is unable to handle the sub-zero temperature and collapses, begging Clark to use his powers to save her. Jor-El forbids him to leave, but finally acquiesces, telling Clark he must return before sunset or there will be dire consequences. Meanwhile, Lana is horrified when she sees two Kryptonian aliens emerge from a spaceship discovered in the remnants of the meteor shower. The two aliens destroy what's left of the town searching for Kal-El.

When Martha comes down with a strange disease, Professor Fine convinces Clark that Jor-El is responsible and that the Fortress must be trying to eliminate the father of Kal-El. But Professor Fine has an ulterior motive which comes to fruition when they arrive.

Clark reveals his secret to Lana, Jonathan and Lex learn the results of the senatorial election, and there is a tragic car accident on the highway that takes the life of someone Clark loves, forcing Clark to appeal to Jor-El for help.

Professor Fine has unleashed a virus that will kill millions. Clark must put a stop to him, while Lex wonders what happens when he will tell Lana his newest secret.

A powerless Clark is trapped in the "Phantom Zone" surrounded by the criminals his father imprisoned there. However, an unexpected ally comes to his aid. Meanwhile, Zod in Lex's body advances his plan to transform Earth into a new Krypton, while using Lana to produce an heir.

Clark and Lois meet Smallville's newest arrival face-to-face, and she has some surprising news. Clark decides to leave Smallville and continue with his superhero training but Jor-el informs him that a new Kryptonian menace has arisen.

Clark hears his mother's voice trapped in Kara's crystal, and releases her. She gives him Jor-El's ring made of Blue Kryptonite, which strips him of his powers.

Chloe begins to notice that Clark's not acting like himself. Bizarro enlists the help of Brainiac.

When Clark wonders if the world would be better off if he never came to Smallville, Jor-El shows him what life would have been like if he had never existed.

Clark takes Chloe to the Fortress of Solitude so Jor-El can heal her after Brainiac replaces her memories with Kryptonian code.

Clark tells Jor-El he’s ready to start his training, but Jor-El sends him back to Metropolis to cut ties with Lois before he can begin. Chloe is shocked when Lois suddenly reappears after having been missing for weeks, but Lois has no recollection of vanishing into thin air with the Legion ring. Chloe begs Clark to use the Legion ring to go back in time to save Jimmy, but he refuses, driving a wedge into their friendship. Meanwhile, Zod arrives at the Luthor mansion...

Tess forces Oliver to come to a Queen Industries gala to put the Board at ease, but things go awry when the Toyman shows up with a bomb and a plan to take revenge on Oliver. The Toyman tells Oliver he must confess to murdering Lex or he will blow the place up. Meanwhile, as part of his training, Jor-El gives Clark the ability to hear other people’s thoughts.

Lois finds Clark's lifeless body and removes the blue kryptonite enabling him to heal himself. However, Lois sneaks away before Clark fully awakens in order to protect his secret. Meanwhile, Chloe is desperate to find Oliver, so she turns to an unlikely source for answers. Jonathan returns to the Kent Farm with a message for Clark, and Tess awakens in a LuthorCorp lab.

Clark takes Lois to the Fortress to get Jor-El’s blessing for their marriage. Jor-El bestows a unique wedding gift on the couple – he gives Lois Clark’s super powers so she can see what it’s like to be him for a day. Unfortunately, the Toyman has returned to Metropolis, so Lois must go up against the notorious villain instead of Clark. Meanwhile, Oliver searches for the Bow of Orion, which he believes will remove the Omega symbol from his skull, and runs into Kara, who is also on a mission to stop Darkseid.