Brad and Amy escaped on a school bus from the agents. After stealing a car, Brad fell asleep at the wheel and Lila gabe Amy assistance over the phone. 

Brad took Amy to his friend, Lacey's house, and she set out to get them a boat to Canada. 

Lila showed up to help, but the agents showed up to take everyone out. Lacey was killed, but Lila escaped out the back. 

Amy handed herself in and she and Brad were bundled into the back of a van. 

Meanwhile, Anthony got prepared to get the treatment, but he had visions of a meeting with Shauna and Tim in which they told him they called the shots in all of this. 

Later, Shauna killed one of the workers at the facility after he tried to goad her into biting someone else. 

In flashbacks, we learned that Jonas started the program when he needed to find a cure for his wife's Alzeihmers.