As part of the penalty for his secret romance with his company's alluring Washington lobbyist Debra Peabody (search), Stonecipher had to forfeit part of a stock award he had been granted just a month before the scandal erupted.
He does, however, get to keep drawing his original $613,000 annual pension, and still owns about $11 million of Boeing stock.
Stonecipher — a grandfather who turns 69 in two months — didn't violate any company policies over his romantic involvement with the 48-year-old lobbyist, company sources said, but it did raise other red flags in the defense industry.
Industry insiders say the scandal spooked the Pentagon because top-secret, classified military projects may have been regular pillow talk during the power couple's trysts.
One defense indorse analyst said Stonecipher "had access to classified materials on our national security, and in the CIA's book that's how he could wind up in a compromised position."
In addition to being CEO, Stonecipher also chaired Boeing's secretive panel that oversaw the planemaker's work on classified military and top-secret national security projects, according to regulatory filings.
Peabody, who's still employed as a vice president in Boeing's Washington, D.C., lobby office, and Stonecipher apparently met on business trips.
He lived with his wife near Boeing's Chicago headquarters.
He and Peabody began their affair after meeting at a corporate retreat in January in Palm Springs, Calif. It wasn't known how frequently they saw each other.
Stonecipher's lost stock award could have reached about $38 million, based on future share prices, according to regulatory filings.
Stonecipher had been retired for barely two years from his jobs as Boeing's president and COO, and remained vice chairman when he was called back to run the company in December 2003 in the middle of a contracting scandal.
The then-CEO Philip Condit (search) stepped down after other executives were fired over contract scandals and probes involving U.S. Air Force projects.
In his comeback, Stonecipher got a salary and bonus of $3 million, plus $336,000 in pension payments that were apart from his original pension he'd been collecting.
He also had received certain stock incentive awards to come back to work, but had to forfeit much of it over his dismissal.
When Stonecipher retired in May 2001, his stock and options were valued at more than $99 million.
He remained active in the company as vice chairman of the board and redeemed many of his options over the next two years.