"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 at the time that preparing future officers for combat should not cross the line into humiliation. He said he wanted upperclassmen to lead by example, not fear.
"We never want to denigrate someone, robbing them of their dignity," he said. "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 Petraeus as commander of the Tampa-based 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 Qurans 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.
The messages from Allen to Kelley, which officials described as "flirtatious" and "inappropriate," led the Obama administration to delay his Senate confirmation hearing as head of U.S. European Command and supreme allied commander Europe.
Colleagues said the communications had been misconstrued, and Secretary of Defense Leon Panetta cautioned against jumping to conclusions.
Panetta ordered the Defense Department's inspector general to investigate the correspondence. But he also told reporters that Allen "certainly has my continued confidence to lead our forces and to continue the fight."
The inspector general cleared Allen last month of any wrongdoing, and the White House asked the Senate to schedule a confirmation hearing.
His retirement Tuesday now leaves the administration to look for a new candidate for the job.