Clark decides that he is ready to start his training at the Fortress of Solitude to become 'Superman'. However, the spirit of Jor-El insists that he return to Metropolis to cut his ties with the people he knows before he begins. Lois reappears in the city with no recollection of vanishing to the future. Her investigation into a monorail crash brings her into contact with a new reporter named John Corben. John is opposed to the "Red and Blue Blur", and has a secret power and identity himself. Meanwhile, Chloe's friendship with Clark deteriorates when he refuses to use the Legion ring to go back in time to save Jimmy. Elsewhere, Oliver turns down a dark path in his quest to rid the world of evil. General Zod makes his entrance at the Luthor mansion before Tess.

After being hit by a truck, John Corben becomes a human guinea pig when his heart is replaced by a machine powered by meteor rocks, which, in turn, gives him extraordinary strength, and he realizes he can use it to catch his prey...the Red & Blue Blur.

Clark, unknowingly, exposes himself to Zod when a virus is released on Metropolis that turns its residents into zombies.

After an accident, Clark (Tom Welling) is able to read Lois' mind, then he asks her out. Meanwhile, a washed up Oliver finds himself in danger.

A mysterious woman forces Oliver to play in a dangerous game of Russian Roulette and then turns up dead. The police believe Oliver is responsible and arrest him, while Clark reluctantly sets out to prove Oliver's innocence. Meanwhile, Lois angrily confronts Clark over his knowledge about Oliver's suicide attempt.

Oliver tries to help a young street girl, Mia AKA Speedy, get out of her dangerous life by offering to train her, but Mia double crosses him. Lois asks Clark to help her land a job as an on-air television host, but the two are shocked when the station wants to hire them as a team.

Jor-El mysteriously arrives at the Kent farm to hide the Book of Rao, but meets Chloe instead. She tells him that his son, Kal-El is on Earth and lives at the farm. Convinced the Blur is Jor-El, Zod enlists Tess's help in finding him to force him to reveal the secret to his powers. Clark realizes Jor-El is alive and on Earth and races to find him before Zod does.

Superhero twins Zan and Jayna (aka: the Wonder Twins) show up in Metropolis to help 'The Blur' fight crime with their combined shape-changing abilities. But the clumsy and naive teenagers end up botching several rescues, landing Clark in hot water with the District Attorney's office. Clark decides to come forward as The Blur to clear his name despite Chloe's protests. Meanwhile, Lois begins seeing a therapist to deal with her growing romantic feelings for Clark, and gets dangerously close to discovering his secret identity.

Tess kidnaps Lois to find out where Lois went after she disappeared for weeks. Lois's memory of the future depicts a Metropolis under Zod's rule and Clark powerless under the red sun, while Chloe forms a resistance group with Oliver. After learning of these future events, Clark makes an important decision about Zod.

Someone with Oliver's skills as an archer take aim at Lois and Chloe.

A man named Sylvester Pemberton tracks down Chloe and tells her he knows about her team of superheroes and needs their help. However, before he can explain who he is, he is attacked and killed by Icicle. Clark and Chloe's investigation leads Clark to the former headquarters of the Justice Society of America, an underground team of superheros, where he meets up with Nelson (AKA: Dr. Fate), Carter Hall (AKA: Hawkman) and Courtney (AKA: Star Girl). Courtney pleads with Hawkman and Dr. Fate to help her catch the killer that is targeting their group but they are reluctant to resume their duties as superheroes. Clark, John Jones, Green Arrow and Chloe team up to help the JSA stop Icicle before he murders another member of the group. Meanwhile, Lois receives a package from a mysterious agency called Checkmate, run by the shadowy Amanda Waller.

Clark meets the sorceress Zatanna (from episode 'Hex') at a comic book convention, where she tells him that her father charmed a copy of the comic book "Warrior Angel" and it holds magical powers. A young boy, named Alec, steals the comic book and develops super powers, transforming himself into Warrior Angel and saving Chloe from a horrible accident who doesn't know about Alec's true origins. Meanwhile, Lois becomes jealous of Clark's relationship with Zatanna.

It is Valentine's Day and while Clark is out on a date with Lois, he unknowingly becomes infected by gemstone kryptonite, which has magical wish-fulfilling properties. Clark mentions to Lois that he wishes they had a more traditional relationship, so Lois quits the Daily Planet, moves in with Clark and starts planning their wedding. Still unaware of his new power, Clark also casually tells Chloe he wishes she would spend more time watching out for him, so an infected Chloe takes his wish to heart and sets her sights on a new target: Lois. Meanwhile, Zod quarrels with Tess as well as his wife, Faora, over the construction of the new solar tower which he hopes will restore his and the Kandorians super powers which will enable them to take over the Earth.

Clark teams up with Zod's wife, Faora, to investigate the abduction of her sister, Vala, and several Kandorians whom have been experimenting with humans in order to find a way to claim their super powers, while Lois herself is abducted by Bernard Chisholm, a former doctor the Kandorians experimented on, claiming that there are aliens on Earth and he wants the skeptic Lois to write an article about it. But when Zod goes off on his own and tries to stop Chisholm, without his super powers, Clark is conflicted whether to save the life of his enemy. Meanwhile, Oliver investigates the disappearance of money from Tess' company accounts and he discovers that Chloe is responsible and using the embezzled money to construction Kryptonite weapons for possible use against Zod and the Kandorians.

Clark and Lois head out of town for a quiet romantic getaway, but their plans are thwarted when they run into Chloe and Oliver at their Bed & Breakfast Inn. The couples' awkward moment is interrupted by the arrival of the Silver Banshee, who sets her sights on Clark and Oliver. Meanwhile, Tess faces off with Zod with a surprising result.

Tess creates an elaborate hoax in order to kidnap Oliver/Green Arrow, and delivers him to the shady head of the secret society Checkmate, Amanda Waller, who tells him that that the government is recruiting him to serve his country. However, Green Arrow escapes before they can learn his identity. After Oliver brings Clark and Chloe up to speed on what happened to him, the three investigate and Clark is surprised to find John Jones investigating Oliver's kidnapping too. Clark senses that John is keeping information from him. Oliver and Clark are shocked when Tess reveals that Amanda is after something called "Watchtower," which is Chloe's code name in the Justice League. When Chloe is captured by Checkmate agents, Waller threatens to kill Chloe unless Clark gives her the names and locations of the rest of the Justice League.

Zod continues to pose as "The Blur" and asks Lois to investigate one of Tess' secret labs. An explosion rocks the lab, and Lois is rescued by John Corben who was a subject of multiple experiments. While investigating the explosion, Clark is exposed to red kryptonite. And infected Clark takes Zod to the Fortress. Tess turns to Chloe for help and they send in Corben to stop Clark from revealing all his secrets.

The new editor tells Clark and Lois only one of them 'imps' may keep his/her job. they still collaborate, hoping a super-scoop should change his mind. An apparent opportunity is when Raymond Sacks, fires as D.A. for ordering a failed attempt at Lois's life, is spared prosecution and throws a nightclub celebration. Clark is warned by Chloe the blur's secret is compromised by impostor Zod's contact with Lois. He discovers Maxwell Lord, a wealthy tycoon and Checkmate king-level rogue, enlists Sacks for a plan to identify the Blur, whom a delivery-boy photographed, so he's captured like several people known to have seen him.

Tess's latest intrusion, at Watchtower, and Chloe's excessive lockout mechanism, lock the pair up, likely to be killed while Checkmate breaks trough the last firewalls. Intrudening the Luthor mansion Oliver faces Zod, whose abusive side reemerges, now with superpowers. Clark must save his friends and hopes to do he same for the Kandorians, one of which carries unsuspecting Zod's unborn child, but the all-round secrecy exacts terrible prices.

Clark is desperate to find the Book of Rao before Zod can find it. If it falls into Zod's hands, he will take over Earth. He's asking Chloe for her help. She is hampered by Tess's ravaging of her Watchtower equipment. Lois tells Clark she has a sure-fire way of getting their jobs back, but he is too preoccupied to listen. Her feelings are hurt. She says she needs a mission in life. In the midst of all this, Clark's mom returns unexpectedly with Perry White, whom she has been dating. Lois is smitten with Perry and shows him her hot lead - a photo of the Red/Blue Blur and tales of an alien race that is looking for the Book of Rao. She holds up a picture of it. Perry's jaw drops. He reaches into his briefcase and pulls out a copy of the same symbol. He tells her that they have a shared story. He is investigating an explosion of a secret government complex in the Rocky Mountains but has been blocked by someone with the code name, Red Queen. Meanwhile, Maxwell Lord has imprisoned Tess, demanding that she hand over the Book of Rao. As Chloe tries to help Clark search for the book, the Red Queen locks her computers. At an uncomfortable "family" dinner, Lois informs Clark that she's breaking up with him. Tess awakes from the mind manipulation that Lord has been using on her to get the Book of Rao. She grabs his gun and escapes. She heads home to get Rao from her wine cellar hiding place. But the real Red Queen - Martha Kent - holds her at gunpoint, knowing she would go for Rao when she fled Lord. Tess is forced to hand it over. Perry and Lois's story collapses, but his good word to the Planet editor gets Lois and Clark their desks back. At the Kent farm, Clark tells his mom that he knows now she is the Red Queen. She answers back that she has never stopped trying to protect him. If he uses the knowledge in the Book of Rao to exile all Kryptonians to another plane, it will exile all Kryptonians from Earth, including himself. She hands the Book of Rao to him.

Zod unleashes his army upon the world, forcing Chloe to call in reinforcements from old friends. Zod tells Lois he is The Blur and asks her to steal the Book of Rao from Clark. Torn between Clark and The Blur, Lois asks Clark to come clean with her about everything but he refuses. Chloe and Oliver attempt to reconnect Watchtower's satellite system in order to fight the Kandorians but to Chloe's horror, Oliver gets caught on site and disappears. Tess attempts to stop Zod but he leaves her clinging to life. Clark and Zod battle for control of Earth.