The first episode tells the story of the meteor shower that hit Smallville and changed life in the Kansas town forever. Clark Kent meets Lex Luthor for the first time and encounters the first in a long line of humans mutated by the strange green meteor rocks that accompanied him on his journey to Earth.
After Lana is almost assaulted by a college student, Clark injures the boy while helping her. When the Kents are sued for damages that could cost them the farm, Clark tries to find a way out of the lawsuit. Meanwhile, Helen's obsessive ex-boyfriend comes to Smallville to win her back but when she turns him down, he stabs her, prompting Lex to take the law into his own hands.
Under the influence of red kryptonite, Clark is following a life of crime in Metropolis while his friends and parents desperately try to find him. Lex is forced to confront his personal demons on a desert island, while Lionel holds a funeral for his presumed-dead son. And Jonathan Kent must pay a high price for the power necessary to bring his son back home.
Clark dreams he is being pursued by a frightened young girl who needs his help. However, after he discovers she is actually a comatose neighbor who should have woken up years ago, he enlists Lana's help to uncover the truth - which puts Lana in grave danger. Meanwhile, Lionel demands that Lex undergo a full psychological evaluation before he hires him.
Perry White, a once promising journalist whose career was destroyed by Lionel Luthor, arrives in Smallville in search of alien stories for a tabloid news show. In spite of being constantly inebriated, Perry believes he has witnessed Clark using his extraordinary speed, so he devises a dangerous scheme to expose Clark's superpowers. Meanwhile, Lex learns that Perry has powerful incriminating evidence of Lionel's shady past.
Clark discovers that Jor-El was on Earth forty years ago. Lana's great uncle, who was convicted of murdering his wife forty years ago, shows her a picture of the man he believes really killed her aunt, and she is shocked to discover the drifter looks just like Clark. Sure that the man is Jor-El, Clark's investigation leads him to a kryptonian medallion that allows him to see bits of the past - and the life that Jor-El started for him long before he arrived on Earth.
Clark is suspicious when Lana suddenly becomes attracted to a fellow student and begins to act rebelliously, which eventually lands her in jail. Clark's suspicions are confirmed when he discovers Lana's new boyfriend has magnetic powers that can move objects and alter human emotions, but when he tries to free Lana from the paranormal hold that is controlling her, she tries to kill him. Meanwhile, Lex discovers Chloe has been delving into Lionel's past and tries to get her to join forces against his dad.
Lex locates Morgan Edge and gets him to admit to dirty dealings with Lionel, but before Lex can take it to the authorities, someone tries to kill him at the mansion. Barely surviving, Lex flees and asks Clark for help. However, when Clark returns to the mansion to investigate he finds nothing amiss, and begins to wonder if it really happened, especially after Lionel announces Lex has had a psychotic break and must be institutionalized.
Three of Clark's former opponents approach Lex to enlist his help in luring Clark to the hospital after they hear that Lionel has requested Lex be given electroshock therapy to erase his memory. However, the plan goes awry when the villains double-cross Lex and use kryptonite to steal Clark's powers. Meanwhile, Lana meets a mysterious stranger in the hospital.
Attempting to stop a robbery, Clark is temporarily blinded when he shoots off a burst of heat vision that is accidentally reflected back into his eyes by a piece of kryptonite and soon realizes his body has developed super-hearing to compensate for his lack of sight. However, as it was in the beginning with his other gifts, Clark doesn't quite have his new power under control.
Clark tells Jor-El he’s ready to start his training, but Jor-El sends him back to Metropolis to cut ties with Lois before he can begin. Chloe is shocked when Lois suddenly reappears after having been missing for weeks, but Lois has no recollection of vanishing into thin air with the Legion ring. Chloe begs Clark to use the Legion ring to go back in time to save Jimmy, but he refuses, driving a wedge into their friendship. Meanwhile, Zod arrives at the Luthor mansion...
After being struck by a truck, John Corben wakes up alone in an abandoned apartment as a man-machine with a Kryptonite heart. Corben realizes he now has superhuman strength and sets out to exact revenge on the Red-Blue Blur, who he perceives to be an irresponsible vigilante. Against Clark's wishes, Lois involves herself in the Red-Blue Blur's investigation, and winds up getting kidnapped by Corben.
Tess forces Oliver to come to a Queen Industries gala to put the Board at ease, but things go awry when the Toyman shows up with a bomb and a plan to take revenge on Oliver. The Toyman tells Oliver he must confess to murdering Lex or he will blow the place up. Meanwhile, as part of his training, Jor-El gives Clark the ability to hear other people’s thoughts.
Oliver is drugged and kidnapped by a woman named Victoria AKA Roulette, who tells Oliver that he’s involved in a dangerous game and must fight for his life. After Victoria shows up dead and Oliver is arrested by the police, he turns to Chloe for help. Meanwhile, Lois berates Clark for not telling her about Oliver's suicide attempt.
Jor-El mysteriously arrives at the Kent farm searching for his son, Kal-El, but meets Chloe instead. 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.
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.
Oliver's past comes back to haunt him in the form of The Dark Archer, Oliver's former teacher, who seeks revenge on his student by taking aim at Lois and Chloe. Oliver faces down The Dark Archer after his former mentor kidnaps Mia AKA "Speedy" but is pushed to his limit and Clark races to stop him from making another deadly mistake.
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 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 Amanda Waller.
Clark meets Zatanna at a comic book convention, where she tells him her father charmed a copy of the comic book "Warrior Angel" and it holds magical powers. A young man named Stephen steals the comic book and develops super powers, transforming himself into Warrior Angel and saving Chloe from a horrible accident.
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.
Bernard Chisholm, a doctor who died and was brought back to life by the Kandorians so they can experiment on him, escapes and kidnaps some Kandorians in order to prove aliens have invaded Earth. Bernard tries to get Lois to write a story validating his claim, but when Lois refuses, he kidnaps her too. In an effort to save his people, Zod poses as a reporter from the Daily Planet and uncovers Bernard’s secret lab. Clark arrives at the lab just in time to see Zod get shot.
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 Green Arrow, and delivers him to Amanda Waller, who tells him that that the government is recruiting him to serve his country. However, Green Arrow escapes before they can reveal his identity. After Oliver brings Clark and Chloe up to speed, 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." 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.
Lois investigates the early prison release of ex-District Attorney Raymond Sacks but he threatens her with a gun when confronted. The Blur saves her, but is captured on film by a delivery guy who plans to sell the photo to Sacks. Lois and Clark each attempt to thwart the delivery of the photo and run into Maxwell Lord, a wealthy tycoon and Checkmate operative, who is trying to learn The Blur's identity to eliminate him. Meanwhile, Chloe discovers Zod's secret.
Much to Clark's surprise, Martha Kent returns to Smallville with her new boyfriend, Perry White in tow. Lois and Perry realize they are both working on the same story about the Red Queen, and decide to team up, which ultimately puts them in serious danger. Chloe helps Clark search for the Book of Rao, which they believe contains information on how to stop Zod and his army.
Lois finds Clark's lifeless body and removes the blue kryptonite enabling him to heal himself. However, Lois sneaks away before Clark fully awakens in order to protect his secret. Meanwhile, Chloe is desperate to find Oliver, so she turns to an unlikely source for answers. Jonathan returns to the Kent Farm with a message for Clark, and Tess awakens in a LuthorCorp lab.
After Lois departs for Egypt, the Daily Planet hires a new reporter by the name of Cat Grant to take her place. An assassin named Deadshot takes aim at Cat but Clark learns the man has a dangerous hidden agenda that involves The Blur. Meanwhile, Carter Hall turns up in Egypt to keep an eye on Lois and he tells Lois about his wife Shayera.
Clark is stunned when Kara returns to Earth and tells him Jor El sent her to stop the dark force that is coming because he doesn’t believe Clark can handle it. Meanwhile, Lois confronts Gordon Godfrey, a shock jock radio DJ who has been crusading against heroes, after he threatens the Green Arrow. However, after Godfrey is possessed by the dark force, he takes Lois hostage and Clark and Kara have to come to her rescue.
In an attempt to cheer up Clark, Lois convinces him to attend their five-year high school reunion. A visit back to the home of the Crows has Clark remembering old times with Lana and Chloe, while Lois is furious that no one remembers her five days as a student. Brainiac 5.0 uses his Legion ring to visit from the future and takes Clark through his past, present and future. He shows Clark what really happened the night Jonathan died, Oliver’s current pain and Clark’s future at the Daily Planet with Lois and his role as Earth’s favorite red and blue superhero.
Lois decides to tell Clark she knows he’s The Blur, but she accidentally activates an ancient artifact that transforms her into the Goddess Isis, complete with superpowers of her own. Oliver and Clark reluctantly decide to ask Tess for help with Lois. Meanwhile, after Cat Grant witnesses Lois as Isis using her superpowers, she decides Lois is the Blur and sets out to prove it.
Clark is concerned about Lois’ safety so he diverts her away from covering the Vigilante Registrations Act by suggesting she cover another story. After he comes clean with her, an angry Lois tells him that she can take care of herself, but when a flat tire strands their car in the middle of nowhere, their plans take a turn for the worse and Lois ends up in serious danger. Meanwhile, Tess searches for a cure for Alexander, who is rapidly aging.
The General and Lucy Lane decide to drop in on Lois and Clark for a surprise Thanksgiving dinner. Clark and the General get off to a rocky start after Lois’ father bashes the superheroes and tells Clark he is trying to pass a vigilante registration law. Meanwhile, in an effort to stop the vigilante registration act from being passed, Rick Flagg lies to Lucy in order to lure Clark away from the farm long enough for him to assassinate the General. Lois is torn between making her father proud and her love for Clark.
In an effort to protect the rest of the team, Oliver decides to register for the Vigilante Registration Act to see what the government plans to do with the new law. As he suspected, it was a trap to lure superheroes to an undisclosed location where he is confined to a jail and subjected to a battery of brutal tests under the supervision of Col. Slade. Aquaman and his new wife Mera team up with Clark to free Oliver. Lois is frustrated when Clark continues to push aside her offers to help the team and sets out to prove she can play with the big boys.
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.
The VRA is in full effect and things take an unfortunate turn of events after the Green Arrow tries to stop a mugging but is attacked by citizens for being a super hero. Clark discovers that the civilians who attacked Oliver were all marked with a darkness tattoo. Carter Hall and Star Girl return to help Clark deal with Slade’s re-emergence after he kidnaps Lois.
Clark, Oliver, Lois and Dinah are released by the VRA after being captured at Hawkman's funeral, but each of them have flashbacks of Chloe holding them against their will. When Chloe returns, Dinah warns the others that Chloe may now be a traitor. Oliver dismisses her concerns, but Clark is unsure if he can trust Chloe after she disappeared without an explanation.
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 gets shot 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.
Clark is shocked to find a mirror box in the barn. Clark Luthor surprises him and sends Clark Kent back to the alternate reality where Clark runs into a very angry Jonathan Kent. Meanwhile, back in our reality, Clark Luthor visits Tess and tells her that if she doesn’t side with him he’ll kill her. Lois asks Emil to help her bring Clark back.
After everything that happened with the VRA, Lois tells Clark it’s best to make “Clark Kent” forgettable and awkward so people don’t suspect he’s The Blur. However, the two are stunned when a fame-hungry superhero from the future, Booster Gold, sweeps into town and begins making saves and posing for press ops, completely winning over the city of Metropolis. Booster begins his campaign to take The Blur’s place as the “World’s Greatest Superhero” and tries to charm Lois into writing a story about him, but she’s not having his antics and begins her own campaign for The Blur. During one of Booster’s saves, an alien weapon in the form of a scarab falls from a truck and fuses itself to a boy named Jaime Reyes, turning him into the Blue Beetle. Unfortunately, Jaime is unable to control the suit and Blue Beetle starts attacking Metropolis.
Tess (Cassidy Freeman) learns that General Slade was found unconscious on a street corner, proof that someone has gained access to the Phantom Zone’s escape portal and sent him back. Clark decides to return to the exiled land to make sure other phantoms are not fleeing and is furious when Oliver tricks Clark into taking him along. With Clark’s powers gone, the two are immediately captured by the Zoners who take them to their new leader, Zod, who is thirsting for revenge on Clark for banishing him to this Kryptonian jail. Meanwhile, Lois learns Clark trusted Tess with a secret, but didn’t tell Lois.
Clark takes Lois to the Fortress to get Jor-El’s blessing for their marriage. Jor-El bestows a unique wedding gift on the couple – he gives Lois Clark’s super powers so she can see what it’s like to be him for a day. Unfortunately, the Toyman has returned to Metropolis, so Lois must go up against the notorious villain instead of Clark. Meanwhile, Oliver searches for the Bow of Orion, which he believes will remove the Omega symbol from his skull, and runs into Kara, who is also on a mission to stop Darkseid.
The story of Clark Kent culminates in this epic two-hour series finale as Clark takes the last step to becoming the Man of Steel. With surprise guest appearances, nods to the first few seasons of the series and Michael Rosenbaum’s return as Lex Luthor, this final episode wraps up a decade-long story following one man’s journey to becoming the world’s greatest superhero.