McDonnell Douglas

In September 1994, Stonecipher was elected President and CEO of McDonnell Douglas, holding this post until its merger with Boeing in 1997. During this period he became much more of a public figure, and even began hosting the company's quarterly video report. He remained on the Board following the successful completion of that transaction, serving as President and COO of the merged entity. In 2001, he was elected Vice Chairman and retired as President and COO the next year, while continuing to serve on the Board as Vice Chairman.^[3]

Boeing

Stonecipher came out of retirement to lead Boeing, following the resignation of Chairman and CEO Phil Condit in December 2003 over several scandals. These scandals surrounded allegations of documents stolen from competitors and the hiring of a government procurement officer who at the time was involved in the United States Air Force's KC-767 contract. Stonecipher assumed the titles of President and CEO, which was not considered an interim appointment as there was no search initiated for a new Chief Executive, while Lewis Platt became non-executive Chairman of the Board.^[5]

Under Stonecipher's guidance, the Air Force lifted a 20-month suspension of Boeing's Launching Systems Group, which had been involved in one of the scandals, allowing them to bid on Pentagon contracts again.^[6] He also oversaw the launch of the Boeing 787 Dreamliner in order to challenge Airbus.^[7] Although not fully evident at the time, the results of major changes to Boeing's airplane program design, sourcing and financing made during Stonecipher's and Condit's tenures would later prove disastrous. ^{[8] [9]} Shares of the company traded as high as $58.74 in 2005, up 54 percent during his tenure.^[10] However, the outsourcing and divestment decisions made 20 years earlier continue to cause Boeing serious problems in 2023.^{[11] [12]}

In a clash of corporate cultures, where Boeing’s engineers and McDonnell Douglas’s accountants went head-to-head, the smaller company won out. The result was a move away from expensive, ground-breaking engineering and toward what many called a more cut-throat culture, devoted to keeping costs down and favoring upgrading older models at the expense of wholesale innovation. It was McDonnell executives who unexpectedly ended up in charge of the combined entity, and it was McDonnell’s culture that became ascendant. “McDonnell Douglas bought Boeing with Boeing’s money,” went the joke around Seattle. Then-CEO Phil Condit was quoted telling reporters to ignore the talk that somebody had “captured” him and was holding him “hostage” in his own office. But Stonecipher cut a Dick Cheney–like figure, blasting the company’s engineers as “arrogant”.

Stonecipher submitted his resignation upon request of the Boeing Board of Directors on March 6, 2005, after an internal investigation revealed a consensual relationship with Boeing executive Debra Peabody. The probe found that Boeing business operations were unaffected, that Peabody's career and compensation were not influenced, and that there was no improper use of company expenses or property. Nonetheless, the board of directors decided that there would be "zero tolerance on breaches of ethics".^[13] His wife of 50 years, Joan Stonecipher, filed for divorce just days after news of his affair became public.^[14] Stonecipher was succeeded as president and CEO on an interim basis by Chief Financial Officer James A. Bell, until Board Member James McNerney was hired on a full-time basis.^[15]