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.

Lex is targeted by a former Belle Reve patient who can move through frequency, and who wants him to come clean about 33.1. Meanwhile, Clark goes to Seattle to hunt down one of the Phantom Zone escapees.