While hiding the spaceship key in the farm's storm cellar, Martha Kent breathes some unknown meteor-rock spores and immediately gets ill. She is sent to Smallville Medical Center under the care of Dr. Helen Bryce, and the results of her blood tests are sent to the Disease Control Agency (DCA). Because DCA agents are coming to inspect the farm and put it under quarantine, Clark and Pete hurry to move the spaceship. Clark inhales some of the spores and also gets sick, weakening him. The DCA agents find the key, so Jonathan Kent must retrieve it from a military base, expecting a miracle to save the lives of Martha and Clark. With Clark having lost his powers, Helen takes a sample of his blood for examination, and begins to suspect Clark's secret. Meanwhile, Lex fears losing Helen when she gets an offer to leave Smallville to study medicine at a prestigious hospital on the East Coast. Lex also finds out about Clark's condition and secretly takes Helen's medical file on him.

When Lana (possessed by Isobel) kills Genevieve Teague by stabbing her with one of the Kryptonian Knowledge Crystals after she attempts to steal it, it triggers a cosmic event that not only severs Lana's link to the spirit Isobel but also sends meteorites from deep space toward Earth and Smallville. At the graduation ceremony for Smallville High, the military arrives to evacuate the town after news that another meteor shower is imminent. Fearing he has a link to the meteorites, Clark goes to talk to the spirit of Jor-El, who informs him that his only hope is to unite the knowledge crystals in the cave. With time running out, Clark sets about locating the final two crystals as meteorites reign down upon Smallville. Lana gives Clark the third stone they recovered from China, which was in her possession all this time, while the second stone is on Lionel's person, which activates. Lex offers to protect Lana and have her flown to New York City, but she gets caught in the meteor shower while riding in a helicopter. Lois manages to get out of Smallville in time, but Chloe stays behind to follow Clark who retrieves the final one from Lionel which hits them with a burst of energy driving him comatose. Chloe helps Clark retrieve the final stone from the Luthor mansion safe after he is immobilized by kryptonite, and helps him escape from Lex. Clark manages to unite all three stones, which transports him to the wild tundra of the frigid North Pole...