Jor-El, the caves, and the Stones of Power
5 episodes of Smallville carry this thread, 5h in all — 4 of them are in The Essentials.
Arc membership is derived from each episode's own summary text, gated to the seasons the sources place each arc in. It shows where a thread is foregrounded, not every episode it touches.
In airing order
A Kawatche grad student gets superpowers similar to Clark's when he picks up an ancient knife found in the Indian caves. Elsewhere, Lana and Chloe plan a surprise birthday party for Clark at Lex's mansion; and Lex wants to sell the Talon.
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.
The town is evacuated on graduation day in preparation for an impending meteor shower, and Jor-El warns Clark that the entire planet is in danger if the three sacred stones aren't reunited.
When Martha is struck by a mysterious flash of light, Clark thinks it may have something to do with Jor-El's prediction that he'll lose someone close to him. He turns to Professor Fine for answers and is told that his mother only has a few hours to live.
The results of the election are revealed, and Clark returns to the Fortress of Solitude to appeal to Jor-El.