After he abruptly resigned due to a relationship with a staffer, Kubasik will not get a bonus and will forfeit unvested stock options. (Jeffrey MacMillan/FOR THE WASHINGTON POST)

Christopher E. Kubasik, who was set to become Bethesda-based Lockheed Martin’s chief executive officer before abruptly resigning last week, will receive a $3.5 million separation payment.

According to a company filing with the Securities and Exchange Commission, Kubasik will not be entitled to a separate bonus for 2012 and will forfeit any unvested stock options, unvested restricted stock units and long-term incentive performance awards for periods that have not been completed.

Kubasik was asked to resign last week after a company investigation uncovered a “lengthy, close, personal relationship” with a subordinate employee, according to Robert J. Stevens, the company’s chief executive. Marillyn A. Hewson, who was in line to become president and chief operating officer, is now set to become chief executive of the defense contractor, effective Jan. 1.

Hewson, who has worked for Lockheed for nearly three decades, has led the contractor’s electronic systems unit since January 2010.

During a call with Wall Street analysts Monday, Hewson and Stevens sought to reassure investors that the transition will be smooth.

“I’ve been a part of the development of the strategy ... for the last eight months,” Hewson said of the transition process that involved Kubasik. The promotion “just changes my role from being focused more internally” to working more closely with the government and Congress and spending time on policy matters.

Stevens said Pentagon officials have been supportive.

“The initial response has been an understanding of the situation that we faced ... and a full measure of support for Marillyn,” he said. “I don’t think there’s apprehension about the leadership change.”