Lex is targeted by a former Belle Reve patient who can move through frequency, and who wants him to come clean about 33.1. Meanwhile, Clark goes to Seattle to hunt down one of the Phantom Zone escapees.

Clark enters a parallel environment in his subconscious where he is powerless, no one believes the truth about him, and things have turned out much, much differently.

When Clark finally discovers Lionel threatened to kill him unless Lana married Lex, he goes after Lionel to silence him once and for all. Meanwhile, Lana tells Lex she is leaving him, and John Jones, the Martian Manhunter, makes a return appearance to help Clark stop Lex, who has captured the last surviving phantom escapee from the Phantom Zone, having possessed a young boy, in order to use its DNA to power him army of super soldiers at his secret lab '33.1'. Clark bids goodbye to Martha as she prepares to leave Smallville for Washington D.C., and Clark finally reveals his secret to Lana to get her to stay in town. But when Lana mysteriously 'dies' in a car bombing, Clark thinks Lex was behind it and sets off to kill him, and has a fateful meeting with the last wraith of the Phantom Zone at Lex's 'Project 33.1' lab at Reeves Dam. Lois goes to Reeves Dam in search of information about Lex's secret lab and is brutally stabbed by a security guard. Chloe finds a piratically dead Lois at the dam where in a moment of weakness, Chloe's secret power is finally revealed.

When Clark Kent confronts Bizarro, the last wraith from the Phantom Zone, the ensuing fight causes the dam to break, unleashing a torrent of water.

Lex hires Dr. Curtis Knox who claims that he can "cure" someone from being a "meteor freak," changing their lives. Chloe takes an interest in this, but Dr. Knox may have another secret as Clark finds out that Dr. Knox is an ageless immortal who needs blood from kryptonite-infected people to keep his young wife eternally young. Meanwhile, Kara makes an alliance with Jimmy to find out where her spaceship crystal is being held, while John Jones warns Clark that Kara is dangerous and tells him to find the Kryptonian crystal before Kara does. Elsewhere, Lana secretly watches Lex through her Isis Foundation to help meteor freaks.

It's been four weeks since the Fortress collapsed and Clark disappeared. Green Arrow calls upon Black Canary and Aquaman to locate the missing Clark Kent. Clark, in the meantime, is powerless and residing in a Russian prison camp in Siberia. With Lex Luthor missing and presumed dead, a new ruthless CEO, named Tess Mercer, is appointed the head of LuthorCorp and moves into Lex's mansion with her own dark plans for Clark and Metropolis. Chloe is kidnapped by a clandestine group that has discovered her special powers and they want to test the limits of those new powers by locating Green Arrow and his friends.

A serial killer is on the loose in Metropolis, and Clark always seems to be one step behind him, while Chloe's paramedic friend seems to think he blacks out and performs the dirty deeds, himself.

Clark discovers John Jones was shot while working as a police officer, so Clark dons the uniform and goes undercover to find the culprit. Meanwhile, Lana confronts Tess and tells her Lex isn't the man she thinks he is. Lana's shocking news forces Tess to reevaluate her position as the head of Luthorcorp.

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.

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 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.