General Allen was leader at Naval Academy

When Marine Corps Gen. John R. Allen overheard a platoon of first-year midshipmen at the Naval Academy shout "kill" during training one summer day a decade ago, he ordered the word expunged from their vocabulary.

The then-commandant explained that plebe summer, when incoming midshipmen arrive on the yard to acclimatize themselves to academy life and begin preparing for careers as officers in the Navy and Marine Corps, was too early to be thinking about the "kill piece" of military training.

Allen, the commander of U.S. and NATO forces in Afghanistan, now is under investigation for emails he allegedly sent to the Tampa socialite described as the "other other woman" in the Petraeus adultery scandal.

The messages, which officials have described as "flirtatious" and "inappropriate," have led the Obama administration to delay his Senate confirmation hearing as head of U.S. European Command and supreme allied commander Europe. It had been scheduled for Thursday.

Allen, 58, married with two adult daughters, has denied any intimate relationship with the woman, 37-year-old Jill Kelley. Colleagues say his communications with her have been misconstrued, and Defense Secretary Leon Panetta cautioned Wednesday against jumping to conclusions about the allegations.

At the Naval Academy, where Allen has spent, cumulatively, nearly a decade of his 40-year career, he is remembered as a standout midshipman, an award-winning teacher and a transformative commandant who worked to usher in a new era of civility and sensitivity at the training ground for future Navy and Marine Corps officers.

Cmdr. William Marks, an academy spokesman, said the consensus is that Allen had a "very successful tour" as commandant of midshipmen in 2002-2003.

The commandant, second in command to the academy superintendent, is analogous to dean of students at a civilian college. Allen, a 1976 academy graduate, remains the only Marine to have held the position.

The esteem is mutual. Allen wrote this year of "our beloved Academy," which he described as a "shining beacon of honor and pride for our nation" where he "amassed countless memories that sustain me and make me proud."

His appointment as commandant was celebrated by Marines, some of whom felt that the elevation of one of their own to second-in-command was long overdue. But then-superintendent Vice Admiral John R. Ryan said he chose Allen against a field of Navy officers on his merits.

"I didn't go about picking John to pick a first," Ryan told The Baltimore Sun at the time.

Ryan said he was won over by Allen's record — he had earned three master's degrees, commanded infantry companies, served as military secretary to the Marine Corps commandant and led the Basic School, a training facility in Quantico, Va. — and by changes he had introduced as deputy commandant.

"He had a couple of ideas on what we could do better in plebe summer," Ryan said. "What impressed me was it wasn't Marine-oriented, it was leadership-oriented."

Allen led a reconsideration of training at the academy, and ordered the end of some of the harsher methods employed by upperclassmen to discipline their younger charges.

Gone was the "spot correction" — the use of push-ups and sit-ups as instant punishment for minor rules violations, the source of the phrase "Drop and give me 20." Some upperclassmen were relieved of their plebe-training jobs after a plebe complained about being screamed at and scolded too harshly.

Allen told The Sun that preparing future officers for combat should not cross the line into humiliation. He wanted upperclassmen to lead by example, not fear.

"We never want to denigrate someone, robbing them of their dignity," he said at the time. "We want parents to understand that when they give us their children, they will be treated very fairly."

Academy officials said the changes were aimed at making training smarter, not gentler. And the brigade appeared to respond; an anonymous survey of nearly 3,000 midshipmen near the end of Allen's first year showed a greater feeling of security and belonging among women and minorities and a declining sense that athletes who broke rules were receiving more lenient discipline than other students.

Allen's tour as commandant was his third at the academy. Raised on his father's stories of Navy service during World War II, the Virginia native arrived at Annapolis in 1972, and would rise to command half of the brigade of 4,000 students. He graduated in 1976 and was commissioned a second lieutenant in the Marine Corps.

After commanding rifle and weapons companies, studying at the Defense Intelligence College and completing a fellowship at the Center for Strategic and International Studies, he returned to Annapolis in 1988 to teach political science and train paratroopers as jump master of the academy.

In 1990, he earned the William P. Clements Award as military instructor of the year, and left to direct the Infantry Officer Course at the Basic School.

He would go on to serve in the Caribbean and the Balkans and, after his tour as commandant of midshipmen — and promotion to brigadier general — in Iraq and Afghanistan.

Allen succeeded Gen. David Petraeus as commander of U.S. Central Command in 2010 and as commander of the International Security Assistance Forces in Afghanistan in 2011.

In Iraq, Allen won praise for ability to work with tribal leaders in the volatile al-Anbar province. He is credited with holding the mission in Afghanistan together amid several challenges. The burning of Korans by U.S. troops and images of Marines urinating on the corpses of Taliban fighters enraged Afghans, and attacks on international forces by the Afghan fighters they're supposed to be training have increased.

Admired by Republicans and Democrats, he was seen as a lock to win confirmation to head U.S. European Command until the FBI discovered the alleged emails to Kelley. Agents discovered the messages while investigating harassing emails to Kelley, allegedly from 40-year-old Paula Broadwell, Petraeus' biographer and reported mistress.

Petraeus, the architect of the surges in Iraq and Afghanistan, acknowledged an affair and resigned as director of the CIA last week.

Panetta has ordered the Defense Department's inspector general to investigate Allen based on communications the FBI has given to the Pentagon. But in his first public comments on the matter, he told reporters in Perth, Australia, Wednesday that "no one should leap to any conclusions here."

Panetta said Allen "certainly has my continued confidence to lead our forces and to continue the fight."

The Associated Press contributed to this article.