As NBC's Kari Huus reports

When the so-called "Jesus rifle" came to light in Jan. 2010, it sparked constitutional and security concerns, and a maelstrom of media coverage. The Pentagon ordered the removal of the secret code referring to Bible passages that the manufacturer had inscribed on the scopes of the standard issue rifles carried by U.S. soldiers into battle in Iraq and Afghanistan... ...The code stamped into the metal of the soldier's ACOG (Advanced Combat Optical Gunsight) ends with the model number with "JN8:12." which refers to the New Testament passage, John 8:12, which reads: "Then spake Jesus again unto them, saying, I am the light of the world: he that followeth me shall not walk in darkness, but shall have the light of life."

The gunsight, produced by the Michigan company Trijicon, can also feature code referring to scripture from the Biblical books of Matthew, Mark, Luke, Corinthians, and Revelations.

When the story first broke in 2010 General David Petraeus, then-Head of Central Command overseeing U.S. forces in Afghanistan and Iraq, declared use of the "jesus scopes" to be "contrary to U.S. Central Command guidance." The United States military must be "sensitive to the cultural and religious norms of the populace we are supporting," stated Petraeus.

But David Petraeus himself has sent mixed messages. The 2005 evangelical Christian book Under Orders: A Spiritual Handbook for Military Personnel, which claims that "Under the rubric of free speech and the twisted idea of separation of church and state, there has evolved more and more an anti-Christian bias in this country", featured a spirited endorsement from General Petraeus, whose plug appeared on the book's back cover, "Under Orders should be in every rucksack for those moments when Soldiers need spiritual energy".

Since 2005, former Reagan Administration lawyer Mikey Weinstein's Military Religious Freedom Foundation (note: I was employed by MRFF in 2007) has been uncovering one case after another of similar abuses.

MRFF's media archives are bursting with stories documenting improper evangelizing in the U.S. military, a number of which were showcased in journalist Jeff Sharlet's gripping story Jesus killed Mohammed: The crusade for a Christian military.

Sharlet's story opens with an incident that occurred in 2004, in the Iraqi holy city of Samarra. One early evening, as the Muslim call to prayer commenced from minarets throughout the city, a Bradley Fighting Vehicle, with "Jesus killed Mohammed" spray painted in Arabic on its side, in giant red letters, rolled through Samarra as an Iraqi interpreter shouted, from the Bradley's turret through a bullhorn, over and over again, "Jesus killed Mohammed! Jesus killed Mohammed!"

As Sharlet described, the pattern extends up to the command level of the Pentagon where, in 2005, a sub-ministry of Campus Crusade For Christ called "Christian Embassy" filmed a promotional video, within the Pentagon, that included the participation of four generals, including then-Acting Secretary of the Air Force Pete Geren.

But the same year Sharlet's story appeared in Harpers, it was revealed, in stories from GQ magazine and the New York Times, that the evangelical Christian messaging went much higher.

In 2003, the cover sheets for daily briefings called "World Intelligence Update", written for then-Secretary of Defense Donald Rumsfeld and other top Pentagon officials, were adorned with Bible quotations.

Described in the GQ story, the April 10, 2003 cover sheet of the top secret briefing, which author Robert Draper stated had been prepared for President George W. Bush, showed Iraqi crowds, jubilant as a Baghdad statue of Saddam Hussein was pulled down, and an image of an Iraqi child kissing an American soldier. Over these images was a quote from Psalms 33:18 - "Behold, the eye of the Lord is on those who fear Him...To deliver their soul from death."

Wrote Draper,

"This mixing of Crusades-like messaging with war imagery, which until now has not been revealed, had become routine. On March 31 [on the intelligence briefing cover sheet], a U.S. tank roared through the desert beneath a quote from Ephesians: "Therefore put on the full armor of God, so that when the day of evil comes, you may be able to stand your ground, and after you have done everything, to stand." "

As MRFF head Mikey Weinstein told NBC, about the continued use of the "jesus rifles",

"It's constitutionally noxious. It's an embarrassment and makes us look exactly like the tenth incarnation of the crusades which launches 8 million new jihadist recruiting videos."

MRFF's core mission is to protect the religious freedom rights of U.S. armed forces service members and in media appearances, MRFF founder and head Mikey Weinstein stresses that the vast majority of the tens of thousands of cases MRFF has taken up since the nonprofit's founding concern complaints from Christian service members who report being targeted and improperly evangelized (in violation of Department of Defense regulations) because they profess the "wrong" sort of Christian beliefs.

The 2009 science fiction book The War After Armageddon, by Ralph Peters, depicts a world in which aggressively evangelical Christian elements in the U.S. military have prevailed, and a military corps called The Military Order of the Brothers in Christ (MOBIC) spearheads a United States crusade, battling correspondingly fanatic Islamic jihadists, to reclaim the "holy lands" of the Middle East, for Jesus Christ and, along the way, kill every Muslim man, woman, and child on earth.

As researcher Chip Berlet describes, the sort of religious eliminationist mentality depicted in Peters' work of fiction was expressed in a 2010 U.S. Department of Homeland Security training held in Las Vegas, during which one participant, asked to recap the message from a speech by an evangelical Christian speaker hired by Homeland Security for the training, Walid Shoebat, summed up Shoebat's message to trainees concerning those identified as Islamic extremists: "Kill them...including the children...you heard him."

The anecdote was from an investigative report from the Boston-based nonprofit Political Research Associates, Manufacturing the Muslim Menace, by Thom Cincotta which, as Berlet describes,

"skillfully exposes how speakers like Shoebat are teaching our public servants to fear Islam and hate Muslims. Cincotta shows how private counterterrorism training groups utilize a network of biased speakers to train law enforcement at every level and in all parts of the country. The response to these trainings has been, unfortunately, quite positive."

Walid Shoebat, whose claims to be a former Islamic terrorist were debunked in a July 13, 2011 report from CNN's Anderson Cooper, was invited to speak at an anti-terrorism conference held at the U.S. Air Force Academy in 2008. Shoebat is one of several "ex-terrorist" evangelical Christians who since September 11, 2001 have been touring the U.S. to warn of an alleged foreign and domestic Muslim menace.

As the press release accompanying the 2010 report Manufacturing the Muslim Menace from Political Research Associates described, Cincotta's report,

"reveals a common set of conspiratorial myths propagated in varying degrees by [anti-Muslim] speakers... These narratives equate Islam with terrorism and depict a covert effort by American Muslim "stealth jihadists" to infiltrate U.S. institutions for the purpose of bringing down American infrastructure and, eventually, implementing Sharia Law."

In May 2012, Wired magazine revealed that an elective course at the United States Officer's Staff College, offered to "senior officers at the lieutenant colonel, commander, colonel and Navy captain level" and taught by Army Lt. Col. Matthew A. Dooley, instructed future U.S. military leaders that,

"a "total war" against the world's 1.4 billion Muslims would be necessary to protect America from Islamic terrorists... Among the options considered for that conflict: using the lessons of "Hiroshima" to wipe out whole cities at once, targeting the "civilian population wherever necessary." "

The May 2012 story came on the heels of a 2011 Wired report exposing extensive use of anti-Islam books, materials, and speakers in FBI counterterrorism training. Course materials obtained by Wired, for its May 2012 story included curriculum material from Colonel Dooley's course that stated,

"Some actions offered for consideration here will be seen as not "politically correct" in the eyes of many, both inside and outside the United States (Examples: Decision Points considered in PH III where Saudi Arabia threatened with starvation, Mecca and Medina destroyed. Islam reduced to cult status). This model presumes Geneva Convention IV 1949 standards of armed conflict and the pursuant UN endorsements of it are now, due to the current common practices of Islamic terrorists, no longer relevant or respected globally. This would leave open the option once again of taking war to a civilian population wherever necessary (the historical precedents of Dresden, Tokyo, Hiroshima, Nagasaki being applicable to the Mecca and Medina destruction DP in Phase III.

As Wired writers Noah Shachtman and Spencer Ackerman described in their May 2012 story,

"For the better part of the last decade, a small cabal of self-anointed counterterrorism experts has been working its way through the U.S. military, intelligence and law enforcement communities, trying to convince whoever it could that America's real terrorist enemy wasn't al-Qaida -- but the Islamic faith itself. In his course, Dooley brought in these anti-Muslim demagogues as guest lecturers. And he took their argument to its final, ugly conclusion. "We have now come to understand that there is no such thing as `moderate Islam,'" Dooley noted in a July 2011 presentation (.pdf), which concluded with a suggested manifesto to America's enemies. "It is therefore time for the United States to make our true intentions clear. This barbaric ideology will no longer be tolerated. Islam must change or we will facilitate its self-destruction.""

Colonel Dooley's elective course has since been terminated, and Dooley removed from his position at the Staff College. In a followup Wired September 21, 2012 story, concerning a threat from Dooley to sue Chairman of the Joint Chiefs of Staff Gen. Martin Dempsey for allegedly violating Dooley's religious freedom, Shachtman and Ackerman reported additional details on Dooley's controversial course: "Materials distributed by Dooley's guest lecturers suggested inaccurately that President Obama is a Muslim. Similar material taught to the FBI in 2011 compared Islam to the Death Star in Star Wars."