03:35 - Source: CNN
US Cmdr. in Afghanistan investigated

Story highlights

Gen. Allen's stellar Marine career makes it hard for those who know him to write him off

Allen has a habit of replying to every e-mail he gets, an official close to him says

Allen did not have an affair with Jill Kelley, the official says

Allen is a married father of two daughters

CNN  — 

A story told about Marine Gen. John Allen while commanding troops in Iraq describes his ability to inspire the loyalty.

A mortar shell landed near a mess hall where Allen was eating, sending a young soldier under the table for cover. Allen, who remained upright during the attack, bent over and said to him, “Son, you’re not going to win the war from down there.”

Allen may be tempted to find cover under a mess hall table this week as he has been entangled in the sex scandal that ended the career of Gen. David Petraeus, who he followed as commander of international troops in Afghanistan.

Petraeus pillow talk: ‘A spy agency’s worst nightmare’

An investigation into “flirtatious” e-mail exchanges between Allen and Jill Kelley, the woman whose complaint about anonymous, harassing e-mails uncovered Patraeus’ affair with Paula Broadwell, has put Allen’s promotion as NATO commander on hold.

The married father of two daughters did not have an affair with Kelley, who is also married, according to a senior official close to the general.

What we know so far

“Allen has never been alone with her,” the official said. “He does everything with his wife.”

Allen, who has a habit of replying to every e-mail he gets, never wrote about sex although he may have said “thanks sweetheart,” in casual e-mail conversation, the official said.

Allen’s stellar career in the U.S. Marines has made it hard for those who know him to write him off because of the controversy.

Allen became the first U.S. Marine to command the International Security Assistance Force - Afghanistan and United States Forces when he took over from Patraeus in July 2011.

Photos: Who’s who in the Petraeus scandal

President Obama will keep him in his Afghanistan post for now.

“He has faith in General Allen, believes he is doing and has done an excellent job at ISAF,” White House spokesman Jay Carney said Tuesday.

“His leadership has been instrumental in achieving the significant progress that ISAF, working alongside our Afghan partners, has made in bringing greater security to the Afghan people in ensuring that Afghanistan never again becomes a safe haven for terrorists,” Defense Department spokesman George Little said.

Fran Townsend, who served as Homeland Security Adviser in the last Bush administration, called him “a competent, respected, admired leader of troops.”

Allen’s military career began when he graduated with honors from the Naval Academy in1976. He returned there in 1988 to teach in the political science department, earning the “military instructor of the year” award in 1990.

Timeline of the Petraeus affair

He became the first Marine to be appointed commandant of midshipmen, the second highest post at the Naval Academy, in 2002.

When Allen was promoted from colonel to brigadier general in 2003, he was made principal director of Asian and Pacific Affairs in the Office of the Secretary of Defense. He held the position for nearly three years.

He served in Iraq as commanding general of the 2d Marine Expeditionary Brigade from 2006 to 2008. He championed the “Sunni Awakening” strategy that organized and paid former insurgents or sympathizers who turned against al Qaeda.

Opinion: 5 things we’ve learned from Petraeus scandal

Allen was posted in Tampa, Florida, as deputy commander the U.S. Central Command from July 2008 until June 2011, when he took over the Afghanistan command.

It was in Tampa that Allen met Jill Kelley, who was already a friend of Patraeus.

Allen holds three master degrees – from Georgetown University, the Defense Intelligence College and the National War College.

The left chest of his Marine dress uniform is covered with military decorations, including the Defense Distinguished Service Medal, the Defense Superior Service Medal, and the Legion of Merit with three Gold Stars in lieu of four awards.

Bergen: Obama’s choices for CIA boss

CNN’s Nick Paton Walsh and Chris Lawrence contributed to this report.