What Lies Beneath

"Lois, would you please just tell me what's bothering you? Is it the Natalie thing? Is it... No! This is what is bothering me! That you left our 15-year-old son home alone to have sex. You're acting like I did something wrong. And you're acting like this isn't a big deal."

- Clark Kent and Lois Lane

Synopsis
Season two opens with the dust still settling in Smallville following the shocking outcome of the confrontation between Tal-Rho and Superman. Lois and Clark struggle as a couple while Chrissy adjusts to running The Smallville Gazette with Lois. Jonathan faces new challenges on the football field, and secrets threaten to destroy Jordan and Sarah's growing relationship. Meanwhile, Kyle grows concerned over Lana's involvement with a new mayoral candidate. Lastly, John Henry Irons and his daughter Natalie attempt to make this new Earth their home.

Main Characters

 * DOD
 * Superman/Clark Kent (Kal-El)
 * The Smallville Gazette
 * Lois Lane
 * Chrissy Beppo
 * Henry Johnson (John Henry Irons)
 * Natalie Johnson (Natalie Lane Irons)
 * Smallville High School
 * Jonathan Kent
 * Jordan Kent
 * Sarah Cushing
 * Lana Lang Cushing
 * Kyle Cushing
 * Kyle Cushing

Villains

 * Bizarro

Other Characters

 * Smallville
 * Jasper Townes
 * Emily Phan
 * Cobb Branden
 * Aidy Manning
 * Smallville High School
 * Gaines
 * Timmy Ryan
 * Malcolm Teague
 * Sean Smith
 * Corey Wellnitz
 * Captain Luthor's A.I.
 * Aidy Manning
 * Smallville High School
 * Gaines
 * Timmy Ryan
 * Malcolm Teague
 * Sean Smith
 * Corey Wellnitz
 * Captain Luthor's A.I.
 * Captain Luthor's A.I.
 * Captain Luthor's A.I.
 * Captain Luthor's A.I.
 * Captain Luthor's A.I.
 * Captain Luthor's A.I.

Teams and Organizations

 * Smallville High School
 * Smallville Crows
 * The Smallville Gazette
 * Sequoia
 * Victoria May's Diner
 * Metropolis High School
 * DOD
 * Defense Threat Reduction Agency
 * U.S. Army
 * Smallville Community Bank
 * Metropolis High School
 * DOD
 * Defense Threat Reduction Agency
 * U.S. Army
 * Smallville Community Bank
 * DOD
 * Defense Threat Reduction Agency
 * U.S. Army
 * Smallville Community Bank
 * Smallville Community Bank
 * Smallville Community Bank
 * Smallville Community Bank
 * Smallville Community Bank
 * Smallville Community Bank

Events

 * Arrival on Earth-Prime
 * Rescue of the North Korean Submarine
 * Earthquakes in Smallville

Species

 * Humans
 * Kryptonians
 * Humans (UE-25)
 * Kryptonian-Human Hybrids
 * A.I.
 * Metahumans
 * Kryptonians (Inverse World)

Objects

 * Clark Kent's Glasses
 * METIT 101 378
 * Kent Farm Truck
 * Auto-Drive RV
 * Superman Suit
 * ELTs
 * Superman Suit
 * ELTs
 * ELTs

Locations

 * Earth-Prime
 * Earth
 * USA
 * Kansas
 * Rice County
 * Smallville
 * Kent Farm
 * Kent House
 * Kent Barn
 * Smallville High School
 * Main Street
 * Sequoia
 * Victoria May's Diner
 * The Hofherr Building
 * Smallville Community Bank
 * Cushing Residence
 * Atlas Pond
 * Shuster Mines
 * New York
 * Metropolis
 * Metropolis High School
 * DOD Facility
 * Shuster Mines
 * New York
 * Metropolis
 * Metropolis High School
 * DOD Facility
 * DOD Facility
 * DOD Facility

Trivia

 * This episode opens directly after, with the later majority of the episode taking place three months later.