In September 1994, Stonecipher was elected president and CEO of McDonnell Douglas, holding this post until the company’s merger with Boeing in 1997. Stonecipher came out of retirement to lead Boeing in late2003. on March 6, 2005, Stonecipher submitted his resignation upon request of the Boeing Board of Directors due to an improper relationship with a female Boeing executive. Boeing said an internal investigation revealed a “consensual” relationship between Stonecipher and the female executive that “would impair his ability to lead the company”. His wife of 50 years, Joan Stonecipher, filed for divorce just days after news of his affair became public.