In August 2018, Ferguson was assigned to the first test flight of the Boeing CST-100 Starliner,[1] although he stepped down from the mission in October 2020.

After a brief period of instruction, he joined the 'Red Rippers' of VF-11 deploying to the North Atlantic, Mediterranean and Indian Ocean on board the aircraft carrier USS Forrestal.

He served one year as an instructor at the Naval Test Pilot School before joining the 'Checkmates' of VF-211 in 1995 and completing a deployment to the Western Pacific and Persian Gulf in defense of the Iraqi no-fly zone on board USS Nimitz.

He briefly served as an F-14 logistics officer for the Atlantic Fleet prior to his selection to the space program.

Ferguson was the deputy chief of the astronaut office prior to his selection to the STS-135 crew and served as CAPCOM for the STS-118, STS-128, and STS-129 missions.

The mission delivered the second port-side truss segment (ITS P3/P4), a pair of solar arrays (2A and 4A), and batteries to the International Space Station.

A total of three spacewalks were performed, during which the crew connected the systems on the installed trusses, prepared them for deployment, and did other maintenance work on the station.

Ferguson made his third and last flight as a NASA astronaut, Commanding STS-135, the final mission of the Space Shuttle.