Zod and the Phantom Zone
5 episodes of Smallville carry this thread, 5h in all — 3 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
Clark is imprisoned in the Phantom Zone, deprived of his powers. Meanwhile, Lex/Zod keeps Lana captive so she can sire him an heir; Lois and Martha crash near the Fortress of Solitude, where Jor-El tells Martha how to kill Zod; and Chloe reunites with Jimmy Olsen.
Clark and Raya face another escapee from the Phantom Zone, Baern, who knows the secret of the Kryptonian Black Box and will be unstoppable if he accesses its power.
Lex disappears in front of Lana's eyes but nobody, including Lionel and Lex's security team, seems to believe her; Clark finds another refugee from the Phantom Zone---and this one eats human bones.
A Zoner called Titan turns up in a secret fight club that broadcasts its battles on the Internet. When Lois investigates, she's kidnapped and forced to participate, and Clark's attempt to save her sparks a surprising turnaround.
In the sixth-season finale, Clark learns how Lionel got Lana to marry his son; Lana tells Lex that it's over; Martian Manhunter helps Clark stop Lex from finding the last Phantom Zone wraith, hoping to keep him from building his army of super soldiers; and Lois gets into serious trouble when she tries to investigate the secret lab.