At the end of Season 8, instead of taking him in, the BGC turn him over to Freelancer Command. Believing Epsilon to finally be taken care of, the Director has to remove the last of the evidence that Alpha was tortured. So he wipes Wash's memories. Somehow Wash escapes (maybe Carolina breaks him out? Or Caboose pesters the others enough to go get Church and grab Wash on the way out?) and it's up to Epsilon to help get Wash's memories back.