A flower that comes from a reopened "Level Three" of the fertilizer plant brings strange reactions from several people, including Jonathan, Lana, and Pete.

The mysterious Green Arrow steals a necklace from Martha, and both Lois and Clark resolve to find out who the vigilante is. While Clark determines Green Arrow's true identity, Lex continues his investigation of the mysterious black box while Lionel warns Lana against him.

After escaping from the Phantom Zone, Raya comes to Smallville to visit Clark. Raya and Clark grow close, and Raya reveals how to repair the Fortress of Solitude. Unfortunately, Baern, another escapee seeks out revenge on Clark and Raya for his time spent in the Zone.

Clark discovers that Lana is missing; Tess reveals what really happened to Lana when she woke up from her Brainiac-induced coma; Tess is shocked by what she discovers in a secret LuthorCorp facility.