Jonathan continues to pay for his deal with Jor-el; Dr. Swann and Lionel continue their infatuations with Clark; Lana and Clark kiss.

What's up with Jonathan: Martha is worried about Jonathan as he works on the roof of the barn, but before she can convince him to come down he hears a piercing noise and falls. Clark is able to catch him and asks him what he heard. Martha said she heard nothing and Clark thinks it came from the octagonal key from the spaceship. Jonathan becomes upset and calls Clark "Kal-el" and tells him to leave him alone.

What's up with Lionel: The phone rings just as Lionel begins to squeeze the trigger of the gun that is in his mouth. He answers the phone and after learning "he's there" puts the gun away and heads to a waiting chopper. He interrupts Clark, who's in the caves trying to talk to Jor-el. Lionel is suspicious of Clark and believes he holds the answers to the mystery of the caves. Later, he tries to get Lex to join him in his search for answers, but Lex refuses.

What's up with Lex: Lex is still helping the FBI make a case against his father. The Feds hear all of Lex's conversations by bugging the mansion and getting Lex to wear a wire. They want to know why everyone's so interested in Clark, but Lex tells them to leave him out of it, he'll help them get his father, but won't help them learn anything about Clark.

What's up with Clark: Clark keeps pressing Jonathan to find out why he's so upset. Jonathan finally explains that his near death experience has left him questioning choices he's made in his life, but he tells Clark he's never regretted taking him in. After they talk, he gives Clark the key and Clark locks it in the barn. When Clark learns his dad has taken off without telling anyone he heads to the Talon and talks to Lana. She reassures him things will work out and in the moment the two kiss. Clark tells Lana he doesn't want to have any regrets but before he can continue she says he should be worrying about his dad and not their relationship. Clark reluctantly heads off leaving Lana wondering if Clark can truly change.

What's up with Dr. Swann: After failing to enlist Lex in his quest to unravel Clark's secrets, Lionel goes to see Dr. Swann. Lionel wants him to explain what's written on the cave walls. Swann says he can't help. He asks Lionel what his motivation is, and guesses correctly that Lionel is dying. Lionel tells him he's sure the secrets locked in the cave can save his life. He tells Swann that he's sure Clark stole the key back and wants him to talk to Clark to help him recover it. Swann refuses, but offers an arrangement.

How it ends: Clark finds Jonathan in a cemetery, by his father's grave. He tells Clark he doesn't know how to protect him anymore. Clark reassures him that's not his job and that he still needs him and so does Martha. When the two make it back to the farm they find it's been torn apart by FBI agents and Martha tells them the only thing they took was the key. Jonathan calms a vengeful Clark by telling him they got nothing as he holds the real key in his hands. Clark finds out from Lex that it wasn't the FBI that raided the farm, but Lionel's men and the Lionel went to see Dr. Swann. Clark confronts Swann about the claim and accuses him of betraying his secret. Swann calms Clark down and says him he's never let Clark's secret leave the building. He also shows Clark a message he's picked up in Kryptonian. The message originated from Earth and simply says "I'm waiting." Swann says he believes it's not meant for Clark.

When Clark gets home he finds out Jonathan has taken the real key and vanished once again. Clark believes Jor-el is trying to contact Jonathan and rushes to find him. Lionel has set up tons of equipment in the caves and scientists work away determined to unlock their secrets. Jonathan barges in with a shotgun and the scientists clear out. Jonathan attacks Lionel and demands he stay away from his son. During the fight the key flies into the wall of the cave. Clark arrives and pulls Jonathan off Lionel just as security forces storm the caves. Before they're able to haul the Kents off, Jonathan warns Lionel if he doesn't let them go, he'll expose him for illegally raiding his farm.

The next day Lana shows up at the farm. Clark tries to get back together with her, but she says she can't continue to stay focused on him because she has to figure out what's best for her. After she leaves, Jonathan tries to comfort his son. As they talk, Clark asks what Jor-el is waiting for. Jonathan tells him it's none of his concern. Then he tells Clark the key isn't in the wall of the cave, but is still out there somewhere. The key appears in a box, in the office of Dr. Swann.