Gen. John Allen, former Afghanistan commander, will retire

WASHINGTON — Gen. John Allen, the top commander in Afghanistan until 10 days ago, will retire from the Marine Corps to help care for his ailing wife rather than accept a White House nomination to be supreme allied commander at NATO, one of the Pentagon’s most prestigious positions.

The Pentagon inspector general cleared Allen last month of misconduct in connection with hundreds of emails he had exchanged with a Florida socialite who cultivated ties with senior military commanders. The investigation had put his promotion on hold since November.

Allen said he was leaving the Marines chiefly to help his wife, Kathy, who has an autoimmune disorder.

“The reasons for my decision are personal,” Allen said in a statement Tuesday. “While I won’t go into the details, my primary concern is for the health of my wife, who has sacrificed so much for so long.”

She “enabled me to serve my country” for more than 35 years, Allen said, adding, “It is profoundly sobering to consider how much of that time I have spent away from her and our two precious daughters. It is now my turn to stand beside them, to be there for them when they need me most.”

Allen’s unexpected retirement leaves the White House with no obvious choice to head the North Atlantic Treaty Organization military alliance at a time when U.S. and NATO forces are trying to withdraw from Afghanistan.

The current NATO commander, Navy Adm. James Stavridis, has held the post since 2009 and was scheduled to step down last summer. Officials said retired Army Lt. Gen. Douglas Lute, a top White House security aide who was passed over for the job last year, may get another look.

President Obama met Tuesday morning with Allen and accepted his request to retire “so that he can address health issues within his family,” the White House said in a statement.

“John Allen is one of America’s finest military leaders, a true patriot, and a man I have come to respect greatly,” Obama said.

Leon E. Panetta, the outgoing secretary of Defense, said in a statement that he would be “forever thankful” that Allen led the war in Afghanistan. “His leadership over the last 19 months will long be remembered as pivotal to this campaign.”

The White House had planned to nominate Allen for the NATO job last year, and Allen had accepted the offer. But the appointment was put on hold in November after he became ensnared in the scandal that forced retired Army Gen. David H. Petraeus to resign as CIA director.

Panetta ordered an inspector-general investigation into emails between Allen and Jill Kelley, a socialite in Tampa, Fla., who had befriended Allen when he served as the deputy commander at Central Command, the U.S. military headquarters for the Middle East based in Tampa.

The FBI uncovered their emails while investigating a separate stream of anonymous emails sent to Kelley about Petraeus. The FBI traced the emails to Petraeus’ biographer, Paula Broadwell, and the CIA chief resigned after publicly admitting that he and Broadwell had carried on an extramarital affair.

The White House planned to go forward with Allen’s nomination after he was cleared of misconduct on Jan. 22. Allen informed Panetta last week that he was thinking of retiring, however.

An officer familiar with Allen’s thinking said the investigation had nothing to do with his decision to leave the Marines. Allen had hoped his wife’s health would improve after he left Afghanistan, the officer said, but it has become clear in recent weeks that her condition has not gotten better.

“He and his wife have been approaching this decision for a long time,” said the officer, who spoke on condition of anonymity to discuss Allen’s reasons. “Their hope was that her condition would improve upon his return home from Afghanistan. It hasn’t. It is for this reason, and this reason alone, that he made the decision.”

david.cloud@latimes.com