Thomas Vega is embarrassed by his father. That's typical of many teenage boys. But Thomas's father is anything but typical; He's conspiracy theorist writing a book about the existence of lizard people in the government. Matters get even more embarrassing when a chance to work on a science fair project with Seraphina Lee, the mysterious new girl at his school, turns into a dinner party with her parents. Her father is a senator. Things take an even weirder turn the day after the dinner, when an old family friend shows up with an ancient book of secrets, and Sera shows up on the run from her own father. Soon Thomas, his sister Venus, and Seraphina are on the run, and go underground (literally) to discover a world of warring factions, extinct life forms, and a plot to destroy humanity.