Clark arrives home at night to a surprise birthday party thrown by Lois, Chloe, and Martha. Martha gives him a present of a birthday card Jonathan had signed before his death, along with a pair of tickets to a Milwaukee baseball game. Clark goes to Jonathan's grave to thank him and leaves the tickets but he turns to see…Jonathan standing behind him. Jonathan apologizes for not being at the birthday party and tells Clark he'll have to "stop it" on his own. Jonathan talks of so many people who will die and warns Clark that Lionel Luthor will do something terrible. Jonathan tells him he must kill Lionel to save the world, then fades off into the mist.
The next morning Martha suggests to Clark he might have imagined Jonathan but Clark recounts how he saw Jonathan once before (in "Void"). Martha wonders at what could be so serious that Jonathan would ask Clark to kill anyone, even Lionel. Lana comes into the Talon to get coffee for Lex and Lois realizes she's dating Lex, although Lana denies it. Lois offers her a sympathetic ear while Clark checks in with Chloe and tells her about the blackmail tape from the warehouse. Chloe agrees they should investigate but wonders what they could find that would drive Clark to kill Lionel.
Lionel is waiting for Lex at the manor and is taking pills. He confronts Lex over his business in Honduras and the fact he and Fine are smuggling deadly viruses into the country. Lionel advises Lex to break up the partnership but Lex dismisses his concerns. After he leaves for a board meeting Lionel has another seizure then grabs a marker and paper and starts writing Kryptonian symbols as his eyes fill with computer data.
Chloe and Clark break into Lionel's office and Chloe finds an appointment Lionel has made with a reporter, Leon Rowland, about a weapon and Chloe wonders if he might intend to discuss Clark.
Lana meets with Lex who admits to her that he's been working on something and warns her that if he tells her, she'll be in all the way. He takes her to a secret LuthorCorp laboratory and reveals he's been collecting deadly viruses and altering them into an ultimate vaccine that works against any disease. He warns Lana that Fine doesn't know about the vaccine and shows her two photos of the ship taken a second apart – Fine is in the first but gone for the second. Lex hoped to buy time to find a weakness but worries Fine doesn't have one. Lana reveals that Lionel told her how to stop the kryptonians, using kryptonite.
Martha arrives home and finds a message waiting for her from Lionel warning he needs to talk to Clark. Before she can call Clark she sees Jonathan sitting in the dark. He asks her how long she's had feelings for Lionel and she assures him he's the only man she's ever loved. Before she can touch him he disappears and reappears behind her, then warns her Lionel plans to kill many more just like he killed Jonathan. He tells her that Lionel must die and then disappears to reappear outside…where he reverts to the form of Milton Fine.
Clark and Martha wonder what "Jonathan" knows while Fine confronts Lex and wonders what Lex is hiding from him. When Fine questions him further, Lex pulls out a piece of kryptonite but Fine is unimpressed, noting he was only made by Kryptonians. He holds a sword-hand to Lex's neck and demands the virus.
Chloe has discovered that Lionel was calling Jonathan regularly up to the time of his death and was at the barn the night of Jonathan's death. Clark sets up a meeting at the barn with Lionel and confronts him over Jonathan's death and Lionel's involvement. He throws Lionel around but Lionel denies knowing anything about any plans to use Clark as a weapon. "Jonathan" shows up to tell Clark to kill Lionel, but Lionel points out "Jonathan" would never make Clark a murderer.
Clark realizes Lionel is telling the truth and uses his heat vision on "Jonathan." "Jonathan" gets to his feet, undamaged, and throws a tractor at Clark before superspeeding off to come at Clark from behind. Lionel, his eyes glazed white, touches "Jonathan" and he reverts into Fine before disappearing. Lionel's eyes return to normal and he has no memory of what happened.
Clark takes Lionel to his office and they conclude Fine isn't a Kryptonian. Lionel insists they not tell Lex anything and Clark agrees, and then Lionel reveals a secret vault containing all of the Kryptonian writing he has been doing. They take the papers to Chloe to scan the information and Lionel reveals the virus is ready, but the warning channeled through him may be of something even more dangerous, but they need to find the lab.
Clark goes to Lana's dorm room and finds the photos she has, and Lana and Lois come in. Lois ducks out and Lana is furious but Clark warns her that Lex is in trouble and needs the lab's location. Fine is at the lab with Lex, who concludes Fine wants the virus to wipe out Earth for when the Kryptonians arrive. Fine warns that he never intended to mass-produce the vaccine but only needs one dose. He merges a bit of his nanotech body with the vaccine and injects Lex with it. Lex collapses and Fine sets the lab on fire. Clark superspeeds in, sees a recovering Lex, then goes after Fine.
The next day Lex has his doctor check him out but the guy finds nothing. Clark arrives to tell him he should have listened to Lionel but Lex denies everything, says they now have the records of the vaccine, and admits he doesn't know where Fine is. As Clark leaves, Lex warns him to come to him, not Lana, if he needs something. The two argue and Lex points out Clark lost Lana all on his own.
At the Kent farm, Lionel arrives to "confess" to Martha that he talked to Jonathan on the phone the night Jonathan died, and that he admitted he knew Clark's secret. He then leaves, telling Martha at least he was honest with her and maybe some day she can forgive him.
Lex and Lana share a meal and as they talk, Lex notices a circular mark on his left wrist. He opens a bottle and cuts his thumb, and looks on in astonishment as the wound heals over. Lex tells Lana he's fine and considers the possibilities. At the barn, Clark contemplates his father's birthday card as Lois shows up to tell him Lana has moved on, which he already knows. Lois assures him that there may be somebody else in the future. Chloe shows up with the cake for a belated birthday and after Lois takes off, Chloe shows him the translation of the symbols, including words Clark recognizes – "Zod is coming."