After being released from a prison in a laboratory of Luthorcorp's Cyntechnics by sympathetic scientist Dr. Hong, former Metropolis High football player Victor Stone is chased by armed security guards and hit by Lana's truck, without any harm. The car is totally destroyed, Lana wounds her forehead and Victor takes her to a hospital. Lana calls Clark, and he meets Victor, who played football against him in high school and died a year ago in a car crash. Victor explained that he became a living machine as part of the machine project researched by the evil Dr. Allister Krieg sponsored by Luthorcorp. Further, he misses his girlfriend Katherine. Clark promises to help him and visits Lex, who lies and tells Clark that he was not aware of the project. Meanwhile, Martha is blackmailed with a DVD showing Clark on a security camera rescuing the unconscious Lana from the warehouse explosion (from episode 'Lockdown') and Lionel offers to help her find the blackmailer.

Clark receives a crystal that sends him and a visiting Lois to the Phantom Zone where they run into Kara. Kara tries to open a portal for Lois before it's too late but Zod's wife, Faora, manages to escape in Lois's body and proceeds to go on a rampage through the streets of Metropolis.

The aftermath of Doomsday's attack on Chloe and Jimmy's wedding leaves Clark in shock, but before he can search for the kidnapped Chloe, an evil being, known as The Persuader, appears and attacks him. Rokk, Imra and Garth, also known as The Legion, step in from the future to help vanquish the Persuader and the group realizes Brainiac has taken over Chloe once again. Meanwhile, up at the Fortress, Chloe, as Brainiac, informs Davis he is Doomsday and was created to kill "the other Kryptonian" and destroy the world.

The story of Clark Kent culminates in this two-hour series finale as Clark takes the last step to becoming the Man of Steel.