College student Caitlin Fairchild is offered a scholarship by the National Security Committee to attend a secret military-based school set in a U.S. desert. While there she meets new friends Percival Chang (Grunge) and Roxanne Spaulding (Freefall). But unknown to them, they are secretly subjects to genetic testing by the school's headmasters, Ivana Baiul and Matthew Callahan, who plot to develop the students into Super-Powered Beings (or go Gen Active) to spearhead an insurrection against the government. The only person standing in their way is Colonel John Lynch, of Internal Operations, an original member of Gen 12, investigates the Gen 13 project and is determined to expose their operations. He introduces himself to Caitlin and revealed that he knew her father, Alex Fairchild.
Soon enough, Caitlin begins to start having headaches and throwing up. She tries making her way to the infirmary before she finds a lab. While searching through its databases for information on her father, she is surprised by Grunge and Roxy, who both were looking for a place to having a midnight snack and smoke respectively without being spotted by the cameras. Unfortunately, they are discovered by a guard, who catches them for entering a restricted area. A fight breaks out when Caitlin tried to explain how she got there. Then suddenly, Caitlin displays superhuman abilities and defenestrated the guard. Her headaches start to get worse before her body mass increased. The trio hide in the air vents as the base goes on high alert. But Caitlin is separated from her friends after the guards drop a grenade down the vent, who soon capture them.
Caitlin is chased through the wastelands by her drill sergeant, Helga in an exo-suit. She is able to knock Helga out, before commandeering her exo-suit to go back to Phoenix base and rescue her friends, sensing them being tortured. Ivana is convinced that they are Lynch's spies and doesn't believe them when they deny it. Soon, she is alerted that Lynch is arriving with a squadron to investigate their illegal activities. After she leaves, Matthew reveals to Grunge and Roxy that he knows that they are telling the truth, revealing himself to have psychic powers. He intends to torture them until they go Gen Active or die. Grunge goes Gen active, able to take on the properties of any objects he touched, and breaks free, knocking out Threshold and freeing Roxy. They then kiss afterwards.
After a skirmish with Ivana, the trio intimidate a pilot to fly a helicopter for them back home. Unfortunately, Threshold prevents their escape and destroys the helicopter. Roxy unknowingly manifests her gravity controlling powers, slowing their fall. Threshold descends to reveal that he intends to overthrow the government that killed his parents. But the trio view him as fanatical and start to fight him. Lynch arrives to defuse the situation, revealing that Caitlin and Threshold are siblings. Lynch explains that the NSC was after the two of them, so their mother turned to her ex-husband Callahan, Matthew's father to get them out of the country. But the NSC killed both of them and captured Matthew. Lynch himself found the infant Caitlin and returned her to her uncle once the government's SPB program was discontinued. Caitlin then soon comes to the conclusion that she was in fact experiencing her brother's memories.
Meanwhile, Ivana had sets the Phoenix base to self-destruct. A landslide is caused by the explosion, heading right for the others. Threshold holds off the boulders, to allow his sister to escape. Because IO doesn't accept resignations, Lynch offers to help train the trio in using their powers to make the world a better place. Caitlin and her friends accepted his offer, before asking Lynch to tell her about her family.