Clark and Chloe have graduated from high school, along with Clark's girlfriend, Lana Lang. After stealing a crystal from Lex, Clark brought it together with two others and disappeared into a vortex that brought him to the arctic tundra, the location of Clark's Fortress of Solitude. Now, Clark is confronted by his biological father, Jor-El (voiced by TERENCE STAMP), who tells him he cannot return to Smallville. Instead, Clark must stay and prepare to save the planet. Also transported to the Fortress, Chloe is unable to handle the subzero 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 recent second meteor shower. The two aliens destroy what's left of the town searching for Clark, whom they know as Kal-El.