As Clark has finally begun dating Lana, Helen Bryce cancels her wedding to Lex after being told to by Lionel. But later, Helen realizes that she loves Lex and they finally get married. Meanwhile, Jonathan and Martha are thrilled to learn Martha is pregnant. The memory/spirit of Jor-El speaks to Clark via the spaceship, telling him he must leave Smallville, his parents and friends to fulfill his destiny. Clark decides to destroy the spacecraft, and the spirit of Jor-El with it, by using Lionel's kryptonite-made hexagon key that he made a copy of off the late Dr. Walden, in order to use it on the cave wall to learn the kryptonian markings. Clark, with Pete's help, steals the key and uses it to activate the spaceship, knowing the kryptonian radiation will destroy the ship. The ship does explode, but the shock wave injures Jonathan and Martha, causing her to miscarry. Chloe, jealous of Clark and Lana's blossoming romance, accepts Lionel's proposal to investigate Clark and gets the job at the Daily Planet. Clark, grief-stricken at the injury he caused his mother, puts on the red kryptonite ring and heads out of town on a motorcycle, planning never to return. Elsewhere, Lex, flying off on his honeymoon, wakes up alone on the airplane that is about to crash in the ocean...

Lex returns to Smalville and the Lex mansion, and invites Dr. Helen Bryce for a second honeymoon while trying to find out if it was her or his father who attempted to kill him. Meanwhile, Clark also returns to Smallville and the Kent farm, but Morgan Edge finds him and threatens to kill Jonathan and Martha in to get what Clark stole from Lionel Luthor's safe, which is the stolen vial of Clark Kent's blood. With the financial status of the Kent family in dire straights, the farm is sold in an auction, but there is a surprise in the end. Also, Lana tries to declare her love for Clark, but he rejects her love out of fear that she may discover his secret. Clark also returns to Smallville High and to the Torch newspaper under Chloe who continues to investigate Clark's origins.