At the manor, Lana is lying in bed awake and Lex comes in to see her. He wonders what’s wrong and notes that she can always trust him. She isn’t initially reassured but appears to consider telling him about her pregnancy, but before she can say anything an alarm goes off. Security mentions Security Code 142 and gets them to the panic room but Lex disappears in a burst of white static. The guards get her into the panic room, while Lex gets up and realizes that the entire manor is abandoned and he can’t leave his library. He then determines he is incorporeal and can’t touch anything.

Clark meets with Chloe at the Daily Planet where she tells him about a ship hit by a meteorite at the same time he returned from the Phantom Zone, and its crew killed. The ship has been towed to Seattle and Clark prepares to go, taking Jor-El’s crystal. Before he can leave, Chloe gets a call from Lana about Lex’s disappearance. Clark decides to go to Seattle instead.

Lionel gets word of Lex’s disappearance and Lana visits him. She accuses him of a conspiracy because security refuse to let her see the security tapes. She relates how she saw Lex disappear and tells him about Security Code 142. He denies knowing about it but promises to investigate and keep her informed. Suspicious, she leaves, and he calls a doctor at Genotechnology.

Clark arrives in Seattle where he’s mistaken for a med student by the attending doctor. She reveals that the entire crew had their skeletons ripped out of their bodies. Two dock workers were attacked as well and whoever is responsible is off the ship. Clark grabs her badge and leaves.

Lana and Chloe go to the manor where the disembodied Lex can’t communicate with them and they can’t see, hear, or feel him. They try to figure out the security code for his computer without any luck and Chloe takes the hard drive with the video footage, while Lana admits she just wants to see Lex despite her previous worries. As they leave, a man appears who can see Lex and confronts him. Lex recognizes the man as “142.” He tries to grab the man but he vanishes.

Chloe calls in Jimmy to help in Clark’s absence. Lana arrives and Chloe shows her the surveillance footage, capturing the scene of Lex disappearing and a static outline next to him. Lana then gets a mysterious call from the man who confronted Lex earlier. She lies to Chloe claiming it’s a security update and goes to meet the man behind the Talon. The man appears and asks for ransom, then tells her about a secret lab where Lex runs experiments on people exposed to kryptonite meteors. He admits he’s a former mental patient and asks her to blow the whistle on the whole thing, offering to take her there. Once she takes it public, he’ll release Lex.

In Seattle, Clark checks out the crime scene and talks to a policeman. After he moves off, the policeman spots a blood trail but is grabbed by the killer. The killer breaks the policeman’s back and then rips out his spine.

Lana and the man, Bronson, reveals how he got his ability and that he can “move through alternate frequencies,” moving to different planes of existence. They go to level 33.1 where they discover the place has been cleared out. Lana wants him to take her to Lex but he fades out, leaving her alone.

Bronson confronts Lex back at the manor and doesn’t believe the millionaire was trying to help him. Lex doesn’t know where the other subjects are and Bronson leaves to go get Lana and use her as leverage.

Jimmy takes Chloe and Lana down to the basement where he’s set up his ham radio and picked up a frequency from the security tape. He descrambles it and determines Lex was in the room on a different “frequency.” While Lana goes back to the study, Clark checks the docks and finds a worker being attacked. He saves the man and tries to use the crystal on the killer but it doesn’t work since he’s not a phantom. He throws Clark away long enough to make his escape.

Chloe hacks into the LuthorCorp operating system to get some floor plans when Lionel arrives as her file are deleted--he's clearly responsible. Lionel asks for help and she reveals she knows about 33.1 from Lana. Lionel leaves but Jimmy reveals he can triangulate and isolate Lex’s frequency.

Back in the study, Lana talks to the unseen Lex and confesses how he’s been so honest to him and she misses him, admitting she’s having his baby. Bronson grabs her and takes her to Lex’s frequency, holding a knife to her throat and demanding 33.1’s location from Lex. Lex still doesn’t know where it is but Jimmy and Chloe arrive and bring them back using the proper frequency. Bronson tries to fade out but Lana grabs him and goes with him. Lex and Bronson fight while Jimmy tries to isolate the frequency and bring them all back. Lex ends up killing Bronson with his own knife then waking up Lana, asking her to confirm she’s pregnant. She does and they kiss, just as Jimmy brings them back.

In Seattle, Clark is searching a warehouse while the killer, Aldar, lurks nearby. The stronger Aldar picks up Clark but suddenly collapses a burn in the shape of a handprint on his back. Clark goes to investigate, stepping on an Oreo cookie, and sees a bald man standing outside. The man’s eyes glow and he says nothing, but flies off into the sky.

Jimmy and Chloe check out the abandoned Lab 33.1 and Jimmy resolves to check things out and Lana arrives. She doesn’t think Lex was involved and figure Bronson was deranged, but Chloe is skeptical.

Lex confront Lionel about how he involved himself in 33.1 without his permission. Lionel admits that Lex has gone further in his research then he ever did. Lionel admits he moved it to a top-security location and will give Lex the coordinates… in return for being made a full partner.

Chloe talks to Clark about what happened to him in Seattle and he admits someone helped him. Clark is reluctant to discuss things and Chloe points out that sometimes even heroes need to be saved.

At the manor, Lex is overly concerned about Lana but tells her it’s the best news he’s ever had. She warns that the meteor freaks are dangerous and in response he shows her how he’s prepared the study with flowers and candles. He then gives her a ring and proposes to her.