Armed with a map and note from her father that she obtained in The Ark Plan, Sky sets off to find Lake Michigan with her friends Todd and Shawn. Unfortunately, they run into scientists from a secret compound in the middle of the lake and are taken captive. Thanks to a young intern, Chaz, Schwartz and Boznic, scientists at the Lincoln Lab, listen to their story, and it turns out that they worked with Sky's father. The lab is trying to recreate some of the dinosaurs that were not previously recreated before the pandemic in order to balance out the population and try to restore some semblance of order to the outside world so that humans might be able to live topside again. Unfortunately, the flash drive of her father's that Sky has found outlines the Noah's ideas to wipe out ALL of the dinosaurs! Not long after finding this out, the lab is attacked by the Noah's marines, and Sky and Todd barely escape with Chaz. Shawn, however, does not make it out. Ivan meets the children outside of the lab, and they all manage to hide away on the Noah's helicopter and make it, undiscovered, to the East Complex in New York City. There, they have to find a way to upset the Noah's plans before all of the work at the Lincoln Lab is negated and the world as they know it crumbles.