A class urging senior US military officers to wage "total war" on Islam wasn't just the work of one misguided teacher. According to an inquiry ordered by the chairman of the Joint Chiefs of Staff, it was the result of "institutional failures in oversight and judgment" at one of the military's top educational institutions.

Those are the results of a months-long, military-wide review into the US armed forces' educational programs. It followed a series of Danger Room articles on counter-terrorism training throughout the American government that sought to portray the world's billion-plus Muslims as enemies of the United States.

The worst of those courses was taught at Joint Forces Staff College in Norfolk, Virginia. Titled "Perspectives on Islam and Islamic Radicalism," the course began years ago as an inoffensive examination of the roots of violent extremism. But in later years, the class was "modified to adopt a teaching methodology that portrayed Islam almost entirely in a negative way," said Col. Dave Lapan, a spokesman for Gen. Martin Dempsey, the nation's top military officer.

The instructor of the course, Army Lt. Col. Matthew A. Dooley, spent weeks arguing that the US was at war with the Islamic faith. In planning for that war's next phases, Dooley invited his students to use the lessons of "Hiroshima" to wipe out whole cities at once, and to target the "civilian population wherever necessary."

Dooley has now been stripped of his teaching position at the college and formally reprimanded – but not cashiered from the Army. Two civilian officials at the college are being reviewed for possible "administrative or disciplinary action," according to Lapan. "A second military officer will receive administrative counseling."

With the exception of Dooley's class, however, the Pentagon review "confirmed that adequate academic standards for approving course curricula, presentations and selecting qualified guest lecturers were in place" at the rest of the military's teaching centers, Lapan added.

That brings the inquiry to a close – without resolving several questions about the course. Nor will the officers exposed to the anti-Islam message receive retraining to correct what the military itself considers an inappropriate and offensive instruction.

Dooley's course, first reported by Danger Room, explicitly encouraged the lieutenant colonels, colonels, lieutenant commanders and captains to reduce Islam to "a cult status" and consider the Geneva Conventions against protecting civilians in wartime "no longer relevant." Dooley discussed apply "the historical precedents of Dresden, Tokyo, Hiroshima, Nagasaki" to achieve the "destruction" of Islam's holiest cities.

Lapan did not explain exactly how the elective turned into what Dempsey's deputy for military education called an "inflammatory" course. The inquiry found that the institutional failings were limited to the Joint Forces Staff College, not the rest of the military's education complex, and any future elective courses on Islam at the college will be "redesigned to include aspects of US policy," Lapan said – namely, that the US isn't at war with Islam.

The inquiry recommended the college strengthen its procedures for "reviewing and approving course curricula while improving oversight of course electives," Lapan said. Additionally, it recommended potential disciplinary action against two unnamed civilian officials and one other unnamed military officer at the college.

As for Dooley himself, he's awaiting his next posting from the Army's assignment branch, weeks ahead of his previously scheduled August 2012 departure from the college. It's unclear what his future holds. He's received an official reprimand, Lapan confirmed – but officers have the right to appeal reprimands. Lapan did not disclose the sort of reprimand Dooley received, so it is difficult to say if the measure will prevent Dooley from future promotions, which is tantamount to firing an officer in the military's "up or out" personnel system.

Yet Dooley's influence may endure. "There are no plans for 'retraining' those who took the elective," Lapan told Danger Room. Nor did the military disclose how many officers had been exposed to the anti-Islam instruction, or even how long the offensive materials were taught, although Dempsey's office previously told Danger Room the inquiry would resolve those questions.

The lack of retraining means that Dooley may ultimately succeed in indoctrinating members of the next class generals and admirals. And the military has undertaken larger retraining efforts. After troops at Afghanistan's Bagram Air Field burned Korans in February, their commander, Marine Gen. John Allen, ordered nearly 100,000 of them re-instructed in how to treat religious materials respectfully. There will be no such effort to ensure that senior US officers disregard Dooley's encouragement to kill civilians.