While Lex continues to investigate the dark past of his father, he meets Morgan Edge with a new face after plastic surgery, and collects evidence to send Lionel Luthor to prison for the murder of his parents. However, a hit man tries to kill Lex in the mansion, but he escapes to Kent Farm. Clark goes to the mansion to retrieve the evidence against Lionel from the safe and finds that there is no hint of the claimed attempt against Lex's life. When Lionel goes to the Kent Farm and tells that Lex is paranoid and delusional over the death of Lex's infant brother years ago, Jonathan and Martha question his sanity. Clark decides to investigate deeper to see if his friend is delusional or there is an evil plot against him. As it turns out, the answer is literally... both. Although Morgan Edge is indeed alive and after both Lex and Clark, Lex's paranoia is real, which leads to him injuring Lana after he suspects her to be a part of the conspiracy against him. Clark then tries to stop Lex from killing Morgan, and in so doing is forced to reveal his secret to Lex.

Oliver tracks down his tormentor Rick Flag, learns he exchanged him for Chloe, who died poisoned, and informs Clark, who helps him work out Chloe actually staged her fake death. On her Daily Planet assignment in Egypt, Lois meets archaeologist Carter Hall ans soon suspects his story about a reincarnated Pharaonic prince is autobiographic. Clark dislikes her staff replacement Cat Grant, but saves her from never identified, yet infallible assassin Deadshot and learns he was the actual target, actually hired by Flag, knowing Superman's weakness is his noble need to protect.

Radio personality Gordon Godfrey becomes possessed by the dark force that Clark was warned about. Godfrey begins waging a crusade against all super-heroes as part of a promotional tour for his anti-vigilante book. Clark is standing on the fringe of a rally when Lois returns to give him a big hug. As they talk, a billboard falls toward the crowd. Clark rushes to catch it before it crushes the crowd. He is not needed. A very visible Kara (dressed in her Supergirl outfit) catches it. She has come back to Earth to tells Clark that Jor-El has sent her to take care of the evil that is coming. Jor-El is sure that the doubt in Clark's heart will allow the dark force to possess him and use Clark's powers as the ultimate weapon. Clark is reluctant to give up on what he views as his own mission. In an attempt to push himself further along, he asks Kara to give him flying lessons. He tries to launch himself from the top of the windmill. It works momentarily, until he then plummets to the ground through the barn roof. Lois learns that Godfrey is planning to reveal Green Arrow's identity online when he posts the final chapter of his book. This will create doubt all over the world about the super-heroes so that he can manipulate them down a new path. Clark and Kara confront Godfrey at a seedy nightclub. Kara's Kryptonian bracelet exorcises the entity from Godfrey. Lois rushes to tell Oliver about the big reveal that is scheduled. It is unnecessary. Oliver has Oliver decided it is best everyone knows the truth. He has scheduled a press conference and announces his identity as Green Arrow.

Clark accompanies Tess, who got childhood nightmares triggered by a mysteriously delivered music-box, to the orphanage where she was left behind by her parents. They find out the hard way 'Granny', who runs it, far from her philanthropic image, in fact ruthlessly rules a brain-washed power girls ring. The general finally sent Lois the video made by her late mother when dying from cancer. Dealing with painful and sweet memories, she ends up digging in Clark's Kryptonian parental antecedents in the fortress.

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