A young naked girl comes out of the woods and uses super-strength to total a car. She then comes to the Kent farm and greats Clark by name, introducing herself as "Kara from Krypton." She claims to have come from the cave and tells the Kents she's here to take Clark home to fulfill his destiny, and warns that everyone he knows will betray him. Lex arrives and Clark offers to testify against Lionel, but Lex figures out Clark hid the knowledge of Lionel's murder of his parents. Clark explains he was concerned for Lex's fate and Lex accepts that.
FBI Agent Loder warns Lionel there's nothing he can do for him, but Lionel is more concerned about Clark and his secrets. Then Lionel reveals to Lex he's dying of his liver disease and nothing can save him, but Lex doesn't buy it. Lionel gives him the medical records but Lex is still determined that he and Chloe put him away, and Chloe vows to testify no matter what.
Kara takes Clark flying to the cave and reveals she's been in the cave waiting until the time is right. Clark declines her offer to go into a passage to find out everything. The next day she tells Jonathan that he "broke the covenant" and reveals that in return for the power he got to bring back Clark, he'd return Clark to his father Jor-El . . . as Loder listens in. Kara senses him and kills him, disintegrating him and his car. Martha is upset that Jonathan made the deal and kept it secret from her. Jonathan goes to Chloe to run Kara's fingerprints, while Lana asks Clark to take her to the airport and tells him to say whatever he has to say before she's gone. Of course, then Kara shows up before Clark can tell her his secret, and puts it off until the next day. Kara warns that he and she are the last ones left and they must repopulate Krypton.
Clark receives a package from Lionel with a key – he confronts Lionel who sends him to the room Lex has been using for his investigation of Clark. Lex explains that he's been concerned with his seeming indestructibility – Clark doesn't buy it and leaves, angry. With everything going on he forgets Lana – Lex is there to say goodbye instead. Clark gets there in time to witness their goodbye hug and leaves without seeing her. Clark testifies against Lionel, but announces his friendship with Lex is over.
Kara is there to comfort Clark and take him to his birth mother. Clark and Kara prepare to "leave" but Chloe identifies the fingerprints as Lindsey Harrison, a girl who was killed on the day of the meteor crash. Jor-El has been using Lindsey as a "shell" to lure Clark in – Jor-El speaks up but when Clark refuses him, Jor-El dissipates him and then hits Jonathan with a bolt of energy and threatens to kill him if Clark doesn't agree. Despite Jonathan's pleas, Clark enters the light and disappears. Martha runs outside to see a Kryptonian symbol burned into the fields, the Sullivans go into protective custody but their new house blows up with them in it, Lionel gets shaved bald, and Lex chokes after drinking a glass of wine. Clark floats in a void while Jor-El promises "He shall be reborn."