After the explosion, Stephen returns to the lair and announces that Hillary is dead but the Founder survived. John made his way back as well, but though he is powerless, he is still useful and comes up with a few helpful suggestions when the paranormals discover that the injections they received have a kill switch. The Founder demands they hand over Roger or he will continue kill them, one every hour.
Jedikiah and Irene work together and find out the tracers run on a network, they also discover the genes responsible for creating paranormals. Stephen and Cara go off to try and stop the signal, John leaves after realizing Cara will hurt herself to protect him and the rest of the group (led by Russell, but controlled by Natalie) decide to take things into their own hands.
The paranormals return Roger to the Founder, who immediately straps him into the Machine and fires it up. Realizing that the human race is about to die, Marla takes Luca away to keep him safe and Cara brings Astrid to the lair and discovers that Astrid and John have formed a stronger bond than she thought. In the end, Jedikiah gets his heart's desire when he takes DNA from Irene and turns himself into a paranormal.