Jedikiah uses his powers to get into Ultra and Roger begs his brother to kill him as it's the only way to stop the Machine. Jedikiah is forced to shoot his brother, but the damage is already done as the Machine sucked up Roger's powers and will soon be ready to kill all humanity. Roger gets Jedikiah out and Stephen manages to escape as well.
The Founder orders Russell and Natalie to go after them.
With only two hours left to save humanity, Stephen wants to become weaponized and finds the serum that will do it. Meanwhile, John finds Astrid and they decide they can't just sit back and do nothing. Cara talks Stephen out of taking the serum and soon everyone works together on a plan to invade Ultra so Stephen can stop the Machine. Once inside, Stephen battles the Founder and throws him into his own Machine. Time was stopped briefly, but soon all is returned as it was.
Natalie takes her revenge by shooting Cara and Stephen is able to reverse time to save her life. Two weeks later, a huge batch of new breakouts arrives, prompting Stephen and Cara to turn Ultra into their new lair. All seems right with the world, except Jedikiah offered John Roger's powers and he accepted.
Jedikiah shows up with his new paranormal super-soldier and offers him, and more like him, to the government's highest bidder. John's memory has been erased and when Jedikiah asks him to help recruit new soldiers (including Cara), he agrees.