Brainiac
6 episodes of Smallville carry this thread, 6h in all — 2 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
Arthur Curry, better known as Aquaman, arrives in town to destroy a new sonar weapon designed by LuthorCorp. Meanwhile, Clark meets Prof. Milton Fine, a.k.a. Brainiac.
Clark is frozen in the Fortress and Bizarro takes over his life, starting with Lana, who shares information about Brainiac. Elsewhere, Grant reveals he is a clone of Julian, and Lex is shocked at his father's reaction to this revelation.
Kara teaches Clark how to fly to help him fight against Brainiac, but Brainiac seems to be a step ahead of them.
Clark searches for Brainiac, who is the only one who can reverse Lana's condition; Chloe accidentally sets off alarms as she hacks into government computers while trying to find info to help Clark; the Department of Security threatens Jimmy with jail time unless he helps them arrest Chloe, while Lex offers to help clear Chloe, but only if Jimmy agrees to be in his debt.
In the seventh-season finale, Brainiac impersonates Kara, whom he has imprisoned in the Phantom Zone, and in her guise he takes Lex to the Fortress for a showdown with Clark. Meanwhile, Chloe is arrested by the Department of Domestic Security; and Lana awakens from her comatose state.
Brainiac slowly takes over Chloe's mind until the only person she remembers is Davis. In an effort to save her, Clark rebuilds the Fortress of Solitude in order to seek help from Jor-El.