A sinkhole opens up on an Oklahoma pipeline drill site, loosing an ancient entity. The three LITs take on their first mission sans Guardian, but there's a wrinkle: The pipeline project is being manned by Stone's estranged father.
- The Alcoholic: Isaac Stone.
- Brutal Honesty: Weaponized to weaken the shapeshifter.
- Double-Meaning Title: What lies beneath the stones—beneath the earth—and what lies beneath the Stone family. Also refers to the other meaning of "lies", particularly those told by Jake Stone.
- I Can Explain: Jacob tries to say he can explain what's going on to Munsi and the sheriff, before realizing that, no, he really can't.
- Imposter Forgot One Detail: Tearjerkingly:Shapeshifter Isaac: I love you, son.
Stone: My dad would die before he would ever say that to me.
- I Thought Everyone Could Do That: Cassandra assumes that everybody works out the size of the set in the back of their heads while watching TV.
- Noodle Incident:
- Cassandra's confessions in the prison are a veritable laundry list of them blurted out in a brief montage. Special award goes to:Cassandra: [excited] ...And as I watched the light go out of his eyes...
- Jenkins briefly mentions an evil mastermind who planned to remove the letter "R" from the English language.
- Cassandra's confessions in the prison are a veritable laundry list of them blurted out in a brief montage. Special award goes to:
- Sealed Evil in a Can: The shapeshifter, until the drilling disturbed its subterranean prison.
- Shout-Out: Cassandra gleefully references Firefly, specifically talking about measuring the width of the Serenity by factoring Nathan Fillion's height and stride with the size of the set.
- Uncanny Valley: The shapeshifter's unnaturally wide smile.
- Voluntary Shapeshifting: Guess who.