( 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 .
Gen. Allen 's stellar Marine career makes it hard for those who know him to brush him off . He has a habit of replying to every e - mail he receives , 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 .