Oliver is tortured incessantly by Rick Flag until Chloe, who used the Dr. Fate's helmet to find him, exchanges herself for him. Awakening in a secret LuthorCorp lab among partial Lex clones, Tess meets young Alexander before the bloodthirsty, dying senior knocks her down and uses Lois, who enabled Clark's healing by removing the fatal blue kryptonite, to set a sadistic trap. Despite his success, Clark lets his confidence be undermined by Jor-El in the ice fortress, but reconsiders after a pep-talk from Jonathan.

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.

Still gravely pondering his place in life, Clark lets Lois drag him along to their Smallvillle high school reunion. Rather than enjoying his hero status, while Lois shines less than she expected, Clark worries when he spots Brainiac, but it turns out he returned from the future with the Legions ring to show Clark how vital his contribution is to prevent a horrible future for him, Oliver, their friends and the world.

Oliver enjoys his new, public role since he outed himself as super-hero, yet misses Chloe desperately and feeling guilty. His example further inspires Clark to tell at least Lois, but just when they meet to that end an Egyptian jewel allows the Pharaonic goddess Isis to take possession of her body, eager to resuscitate her beloved Osiris, all required being at hand from a major exposition in Metropolis, but that would also revive his realm, hell, on earth. Tess, who is otherwise preoccupied with Lex's boy-clone Alexander, joins Oliver and Clark at Watchtower, where she proves herself able to fill in for Chloe IT-wise. Even with that invaluable research, Clark nearly perishes in his supernatural duel with Isis. Cat get caught in the fight and mistakenly believes Lois is the evil Blur.

Clark examines a rural hamlet where blue kryptonite in the water has no known negative effects. However when a bell rings, tho local deputy regretfully knocks out the nosy reporter 'at the wrong time and place'. Lois has a car crash nearby and is nursed by an Amish family. Yet when she wants to leave, she discovers their chilling true intention, as the extremely aberrant sect does with one female every year. In the Luthor mansion, Alexander insists to be called Lex and his aging condition requires 'regular' birthday parties. Mercer's plan to give him a cure if the original lex's research allows so is reconsidered as she realizes this clone may be too perfect.

Clark is far from impressed that Lois barely dares rebuke her kid sister's mean pranks on both of them, while squirming for each, even offensive, whim of Pa, full general Sam Lane, as their Thanksgiving guest. Clark firmly but politely hosts the Lanes, while reasoning against the general's support for a bill to make 'registration' compulsory for superheroes, an obvious trap given the congressional supporters' antecedents. While Oliver investigates them, Clark saves everybody from proponent Rick Flag's Machiavellian rocket attempt on the general's life. Only when Lois finally sides with Clark against Pa, he reveal his ulterior motive for exaggerated rudeness.

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.

Oliver tests the Vigilante Registration Act by outing himself at a press conference, praised by the general in charge. As feared, he's tortured in a secret prison to turn on his superhero friends. Tess helps work out the design from Luthor plans for an underwater top-security facility, build in sixfold. Aquaman 'A.C.' Arthur Curry and his new wife Mera discover and penetrate the one Oliver is held in, but the general rather starts auto-destruct. Clark remains cautious and flashes to the rescue but has to deal with a specific counter-measure.

Tess acquires a Kryptonian box that once belonged to Lionel Luthor. When Clark accidentally activates the box, he's transported to a parallel universe where Lionel found Clark in the cornfields instead of the Kents. In this universe, Clark Luthor is a murderer and Lois is engaged to Oliver and both of them hate Clark. Clark must be careful not to tip off Lionel that he's not his son while trying to figure out how to get back to Earth where the monster Clark Luthor was transported in his place.

As the VRA threat intensifies, Clark takes initiative by closing down watchtower and declaring the League go officially underground, but will this be enough to stop Lt.Trotter and Slade Wilson aka Deathstroke from exposing them? Tensions rise in this mid-season finale.

Clark, Oliver, Lois and Dinah are back home after long VRA captivity, with confused memories and robbed of all superhero-powers. They believe they have been tortured in an experimental lab by none other than Chloe, hence fear she switched sides. Then she, or rather her avatar, appears in dreams to each of them, claiming they only lost their powers in a virtual illusion, which can nevertheless kill them for real. She calls upon them to trust her, break the virtual spell by believing it fake and thus escape back into reality, with Rick Flag's team. Oliver does so quickly, and is reunited with his true love. Clark wants to, but finds it extremely hard, until Lois joins in.

Clark is surprised to see Martha on the news speaking at a pro-vigilante rally. However, surprise quickly turns to horror when he and Lois watch as Martha is injured in an attack on national television. Meanwhile, Lionel reveals himself to the world and reclaims LuthorCorp from Tess and Oliver. Lois and Chloe decide to cheer Clark up by showing him videos from thousands of vigilante supporters professing their support for The Blur.

Chloe and Oliver are mistaken for FBI agents investigating Desaad's recent string of murders and the pair are kidnapped by Desaad's minions. Desaad tries to infect Chloe with the darkness. Meanwhile, Lois tells Clark he needs to be more careful with his identity and suggests a disguise.

After Zatanna sends a magically spiked bottle of champagne to Clark and Lois for their bachelor/bachlorette parties, the gang blacks out after the toast, only to wake up the next morning and realize they can't remember anything about the night before. While trying to retrace their steps, Lois realizes she lost her engagement ring and drags Oliver back to the Fortune Casino where she thinks she lost it. The two run into Fortune, the eccentric casino owner, who accuses them of stealing money from him. Meanwhile, Clark tells Chloe he has a memory of stealing an armored truck the night before.

Lionel and Tess go head to head in a battle for the Luthor name. Clark and Lois are stunned by Tess' latest present to them.

Clark Kent is in nostalgic mood after Martha signs over the deed to the farm as a wedding present, wondering whether it suggests he and Lois should sell and move. Clark Luthor surprises him, using the mirror box and shattering it after having sent Kent to his world, then fool everyone for a while, in search of bloody vengeance on at least one Luthor. Kent finds himself, public enemy number one against whom everyone caries green kryptonite, at Oliver's funeral, where a bitter Jonathan scolds the 'scrooge'. Recognized and helped by the other Lois, he seeks to appease hatred and find a way back. Dr. Emil Hamilton frantically tries to repair the mirror-box, just in time.

Clark gets an inverse make-over from Lois, in order to become a gray mouse when the Blur goes public. Just then, a flashy media-hungry new superhero emerges: Booster Gold, who systematically steals the show. Clark discovers Booster came from the future with a Legionnaire's ring, probably stolen. Generally bullied, shy schoolboy Jaime Reyes is inadvertently infected with the alien scarab which Booster was hired to retrieve for industrialist Ted Kord, hence transformed into the Blue Beetle, an uncontrollable monster. Clark could just expose Booster as a fake coward, but chooses to educate him in superhero ethics.

After the banished General Slade is found on earth, Clark realizes the Phantom Zone portal must be open and decides to go close it, however dangerous as his super powers don't work there. Oliver was denied coming along but managed by surprise. The heroes find the zone under the rule of General Zod, who looks forward to his revenge for both worlds on Clark and was promised full dominion by Darkseid if he eliminates the great Kryponian adversary. So Clark is forced to enter Zod's arena's mortal gladiator combat, while Oliver is offered an alternative and reminded of being Omega-branded already, which no earthling knows yet. In the Watch Tower, Lois discovers the three hours portal destruction 'safeguard' Clark ordered Tess to trigger and fights it.

Searching for the Bow of Orion, the only known means to stop the Darkness, Oliver and Kara independently reached the same booby-trapped underground sanctuary. Kara got herself trapped, but Oliver rescues her in Indiana Jones style. Together they decipher and follow the clues to the bow, only to be get a bitter surprise. Meanwhile instead of giving his blessing in the fortress, Jor-El temporarily transfers Clark's super-powers to his already far too cocky bride.

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