When you're riding the elevator in the Dark Energy level you hear Breen saying "It's me you should be considering, I can still deliver Earth but not without your help".  So, I think the Combine get whift of Gordon's skills and request his services.
I think in Aftermath, Dr. Breen forcibly becomes your ally. An unexpected twist me thinks.
				
			I think in Aftermath, Dr. Breen forcibly becomes your ally. An unexpected twist me thinks.