Jedikiah needs someone to fund his work. An he needs someone will to provide test subjects to allow him to figure out a way to permanently gain powers. A military program aiming at producing super soldiers is the perfect cover operation for his aims.

Jedikiah either purposely or accidentally wiped John memories. I’m going with the second option.

I hope the tomorrow people are smart and decide to work with the government to gain money and resources to allow them to build themselves a new lair and safe haven.