Finishing ninth in the country in rushing yards, he and teammate Fred Tesone formed one of the top rushing tandems in the nation as the two combined for 2,528 yards, outrushing their opponents by over a 2-to-1 margin and helping the Pioneers to a 9–1 record, the first outright conference championship since 1917 and the second-best season in school history.

He was succeeded in command of the 2nd Brigade by a fellow future four-star general, then-Colonel Colin Powell.

Mahaffey's other assignments included Division Operations Officer for the 101st Airborne Division, Assistant Commandant of the United States Army Infantry School; Deputy Commanding General of the Combined Arms Combat Development Activity; and Deputy Chief of Staff for operations for the Army.

Mahaffey was promoted to four star rank in 1985 at the age of 51, making him one of the youngest four-star generals ever.

Diagnosed with cancer while on active duty, he died at Walter Reed Army Medical Center on 13 October 1986, at the age of 52.