With Peter's removal, Jones appears to have survived the portal crossing and is present in the alternate universe and working against both universes with a new prototype of shapeshifter; the alternate Broyles and Brandon appear to have under his control.
With Peter's removal, Jones appears to have survived the portal crossing and is present in the alternate universe. He is revealed to be behind the "Human Shapeshifters" that are plaguing both universes and the alternate Broyles and Brandon appear to be under his control.