The day after Dr. Swann dies, Clark receives a note from the professor leading him to a message from Jor-El that instructs him to find two sacred stones. Meanwhile, Jason and Lex are in China on a related mission; and Lana learns that the witch Isobel has been trying to find the stones by using her as a vessel.

A kryptonite-based explosion at the Luthorcorp lab creates an evil clone of Lex, and the sinister twin tries to prevent the process from being reversed by taking drastic measures, which include imprisoning Lex in the basement of his own mansion.