Recently stripped of his chairmanship and an unusual incentive plan, Chesapeake Energy CEO Aubrey McClendon apologized to investors during a conference call today. “I am deeply sorry for the distractions over the past two weeks,” he said during the discussion with analysts.

Accompanied by CFO Domenic Dell’Osso and the company’s chief operating officer, McClendon immediately addressed that elephant in the room before delving into Chesapeake’s disappointing first-quarter results, including a net loss of $71 million.

Indeed, the past several days have brought controversy to the gas producer amid investor concerns over the company’s governance practices and McClendon’s integrity. It began with an April 18 Reuters article that questioned whether McClendon’s personal investments have created conflicts of interest. Chesapeake is now dealing with regulatory scrutiny of the CEO’s choices, shareholder ire, credit-rating downgrades, and an amended employment arrangement for McClendon.

The controversy surrounds a 10-year incentive deal Chesapeake made with McClendon in 2005 that gave him a 2.5% interest in the company’s wells. He used this stake as collateral to borrow as much as $1.1 billion over the past three years from third parties, leading to debate as to whom McClendon is ultimately beholden, his lenders or investors. Details of this arrangement were not previously disclosed to shareholders.

Last Thursday the board of directors announced that the deal, which was set to end at the end of 2015, would be cut short by 18 months. The company also recently disclosed that the Internal Revenue Service is looking at the arrangement, which it calls the Founder Well Participation Program (FWPP). “We have been in discussion with representatives of the IRS and believe that resolution of these issues will not have a material impact on the company,” Chesapeake said in an amended 10-K filed earlier this week.

On Wednesday’s call, McClendon said the FWPP gave him “skin in the game,” meaning his priorities in terms of the company, which he co-founded, should not be in question. He also acknowledged that the board is searching for a nonexecutive chairman although he is keeping the title in the meantime. In recent years, good-governance advocates, such as GMI Ratings, have criticized companies that don’t split their CEO and chairman roles, an increasingly uncommon occurrence.

Beyond the CEO’s reputation, the executives had several other assurances they needed to make on the call. In addition to the $71 million loss, the company decreased its operating cash-flow projections for the year. Still, Chesapeake plans to stick to its plan to cut its debt by $9.5 billion by the end of this year, in part by selling assets. It’s been hurt by “extremely low” natural-gas prices, according to McClendon, who dominated the call.

In the few remarks he made, Dell’Osso explained that Chesapeake removed its hedges on oil and gas last fall amid concerns over the Greek debt crisis, a move that in retrospect the company would have done differently had it known an abnormally warm winter would continue to keep gas prices down. “Right now we’re certainly focused on the fact that gas has been weaker than the entire market expected it to be in 2012,” he said.

Clearly, the executives have had several regrets as of late. “We appreciate you hanging tough with us,” McClendon said to investors.

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