Well as of last episode, it was revealed that government employees, outside of Fowler, are now aware that two humans, Jack and June Darby, have knowledge of and are interacting with the Transformers. Fowler's troops saw Arachnid and Arcee interact with Jack and June first hand. Which poses a problem for Fowler now. It was hinted at very strongly in the Darkness Rising series that Fowler, though he initially intended to, decided not to reveal Jack's, Raf's, and Miko's interactions with the Autobot's to the government when he stated that he owed the Autobots for saving his life. Well now that his troops are aware of at least Jack's and June's interaction with the bots, it's very possible Fowler's superiors know as well. So are they going to order Fowler to remove at least Jack and June from the Autobots and place them in some kind of witness protection program?