Lois and Clark go to the sight of the explosion to investigate Chloe's death, but a helicopter arrives and drops off some men. Clark defeats them and crashes the helicopter with his heat vision while Lois defeats a third man and they both flee as a military officer with "Lane" on his uniform steps out and orders his remaining man to find them.
Lois has moved in with the Kents and she and Clark have dueling shower privileges, which leads to them having an awkward conversation with Jonathan and Martha spots them, which in turns leads to a discussion about Clark crashing the helicopter. Lex has another enigmatic conversation with Lionel about how he can no longer trust anything. In Paris, Lana notices the similarity between the symbol on her back and returns to Smallville and meets with Lex, renting the apartment over the Talon.
Lois goes to dig up Chloe's grave and confirm Clark's assertion - she finds the grave empty and is then attacked by a mysterious man who can turn his hand into a weapon. Lana shows up and rescues her and the man escapes. The two of them meet up with Clark and awkwardness ensues. Later in the barn, Lois and Clark are talking when the helicopter returns and the army officer shows up...who Lois introduces as her dad.
General Lane leaves shortly thereafter and Clark confronts Lex, who denies everything...but one of Lane's cigars is present. While Clark and Lois separately break into the nearby military base, Lionel is almost killed by a fellow prisoner in the shower. Lois and Clark discover that Lois' father is meeting with a "Nellie Bly" weekly and Clark concludes it is Chloe. He goes to the address only to find dead FBI agents and Lex.
Lex tells him everything, and reveals that thanks to a tracking bracelet he knows Chloe is at a nearby factory. In prison, Lionel meets with the assassin, Trent. Trent tries to hold him up for more money but Lionel lays a little father-imaging on him and the killer goes off to dispose of Chloe. Clark speeds to the factory and stops the killer as he prepares to off Chloe. Lois hits Trent with an electro-stunner and with a little secret assist from Clark's heat vision, knocks him into a smelting pit.
Lionel is convicted on Chloe's testimony and Clark is more convinced then ever that Lex is the great evil who is prophesied to battle him, despite Jonathan and Martha's doubts. He then meets Lana in the cave, who is there to investigate the symbol on her back. Lex is there to gloat as Lionel goes into the general prison population, and Lana's boyfriend Jason follows her to Smallville so they can be together.