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.
Zod and his soldiers release a virus into the air that turns humans into zombies. The only way to stop it is to make an antidote from the blood of another Kryptonian. After Lois is infected, Chloe pleads with Clark to donate his blood to stop the epidemic, even though it risks outing him to Zod.
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.
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 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.
Tess breaks into Watchtower, triggering an elaborate security system that Chloe installed, ultimately trapping the two women inside. Clark realizes Zod has given his soldiers super powers.
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.
When Zod and the Kandorians launch their brutal attack on Earth, Chloe calls in some old friends to join the fight against the aliens. Clark and Zod face off in an epic battle for the control of Earth.
