Clark is in his barn one moment... and the next finds himself in a psychiatric hospital where he discovers he's been suffering from delusions that he came from another planet and has super-powers.

Clark discovers the reason Lana married Lex then and sets out to kill Lionel. Lex tries to use DNA from the last phantom to power his super-soldiers. Lois goes to a dam to search for Lex's lab but is caught by a security guard and fatally injured. Chloe's power is discovered.

During Clark's battle with the last Phantom Zone wraith, Lex is rescued by a mysterious woman. She then goes to the Kent farm and reveals she is Clark's cousin, Kara, from Krypton.

Dr. Curtis Knox says 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.

Green Arrow calls upon fellow heroes Black Canary and Aquaman to locate the missing Clark Kent, last seen in the Arctic. The Martian Manhunter also joins in to help out.

Clark believes a recent attack in a theater may be the work of a serial killer; Davis fears that his blackouts could mean that he is the killer.

Clark learns that John Jones was shot while working as a police officer; Lana tells Tess that Lex isn't the man she thinks he is, forcing Tess to re-evaluate her position as head of Luthercorp.

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.

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.