When Army Specialist Jeremy Hall declined to participate in a Christian prayer ceremony to commemorate Thanksgiving in November 2006 he said he was alienated by his staff sergeant and subjected to vicious personal attacks for stating that he did not believe in God.

Determined to find soldiers who were also atheists, Hall organized a meeting for freethinkers at Combat Operations Base Speicher, Iraq. He said he received permission from the Army chaplain stationed at Speicher to post flyers to publicize the gathering.

But just minutes after the soldiers convened their first meeting last July, Army Maj. Freddy Welborn burst into a room where the soldiers gathered, broke up the atheist meeting and allegedly threatened to block Hall’s reenlistment in the Army and have charged brought against him for violating the Uniform Code of Military Justice.

Fearing that higher ranking Army officials would not come to his defense, Hall contacted the Military Religious Freedom Foundation (MRFF), a watchdog group whose core mission is to force the military to adhere to the constitutional provision mandating the separation of church and state.

So Hall and MRFF filed a lawsuit last September against the Pentagon, Welborn, and Secretary of Defense Robert Gates, for allegedly violating the soldier’s First Amendment rights and for permitting a pattern of fundamentalist Christianity to permeate throughout the military. The complaint was amended in March to include new allegations alleging that Hall’s promotion in the Army was withdrawn because of he sued the military.

Last week, the Justice Department filed a response to the lawsuit-a massive document exceeding 300 pages that essentially says the lawsuit should be dismissed because Hall “failed to exhaust intramilitary remedies, and assert claims that are nonjusticiable.”

“Rather than filing a complaint with his chain of command – or his unit’s Equal Opportunity Advisor, or a Chaplain, or an Inspector General, or anyone else authorized by Army regulations to field such a complaint ¬ Specialist Hall contacted the Military Religious Freedom Foundation, which filed a lawsuit in this Court last September,” the government’s motion to dismiss states. “Thus, the Army was deprived of the opportunity to promptly investigate the alleged misconduct and take appropriate disciplinary action; Specialist Hall missed out on the most efficient way to resolve his complaint; and this alleged incident – which took place in a war zone nearly a year ago – remains the focal point of the present dispute.”

Mikey Weinstein, who worked as a White House attorney under Ronald Reagan, was general counsel to H. Ross Perot, and was formerly Air Force Judge Advocate General (JAG), is the president and founder of MRFF. He said the Army made it incredibly difficult-and other soldiers who may have had similar experiences-to file grievances against the military because senior officials have encouraged lower ranking soldiers to embrace God, have permitted proselytizing and have been vocal about God’s role in shaping their own lives.

“This cancer of fundamentalist Christian tyranny is so pervasive that it is quite literally omnipresent in the U.S. military,” Weinstein said in response to the Justice Department’s motion to dismiss the case. “Trying to go “up the chain” or to the [inspector general] or the MEO is useless and generally results in harsh subtle and not-so-subtle retaliation and reprisal. It’s the very reason we fashioned our federal lawsuit to show a pervasive and pernicious pattern and practice of universal unconstitutional rape of the religious liberties of our honorable and noble U.S. servicemen and women. Quis custodiet ipsos? Who will guard the guards? MRFF will because no one else can.”

In it’s motion to dismiss, the Justice Department says Weinstein’s claims of a “pattern and practice of impermissible support for religion within the Department of Defense” is a “red herring.”

“Plaintiffs identify no person, least of all Specialist Hall, who is affected by the alleged practices, and these allegations are precisely the kind of generalized grievances that are routinely rejected by the federal courts,” the Justice Department’s response states. “Shorn of this window dressing, Specialist Hall’s central allegations are not systemic problems, but isolated incidents that implicate the Army’s authority to regulate the discipline and composition of its forces.”

Weinstein disputes the government’s claims that the matter is an isolated incident. He said his organization has received more than 8,000 complaints from active duty military personnel who claim they are being force-fed fundamentalist Christianity and are routinely subjected to proselytizing. Weinstein said he intends to file additional lawsuits in the months ahead to support these claims.

Additionally, Weinstein points to a report released last August by the Pentagon’s Inspector General that was highly critical of senior Army and Air Force personnel for participating in a video to promote a fundamentalist Christian organization while in uniform and on active duty.

The 47-page report recommended that Air Force Maj. Gen. Jack Catton, Army Brig. Gen Bob Caslen, Brig. Gen. Vincent Brooks, Maj. Gen. Peter Sutton, and a colonel and lieutenant colonel whose names were redacted, “improperly endorsed and participated with a non-Federal entity while in uniform” and the men should be disciplined for misconduct. Caslen was formerly the deputy director for political-military affairs for the war on terrorism, directorate for strategic plans and policy, joint staff. He now oversees the 4,200 cadets at the US Military Academy at West Point Caslen told DOD investigators he agreed to appear in the video upon learning other senior Pentagon officials had been interviewed for the promotional video.

The inspector general’s report recommended the “Secretary of the Air Force and the Chief of Staff of the Army take appropriate corrective action with respect to the military officers concerned.”

The Army generals who appeared in the video appeared to be speaking on behalf of the military, but they did not obtain prior permission to appear in the video. They defended their actions, according to the inspector general’s report, saying the “Christian Embassy had become a ‘quasi-Federal entity,’ since the DOD had endorsed the organization to General Officers for over 25 years.”

It’s that type of thinking, Weinstein said, that led Hall to believe that he would face retaliation if he filed complaints with superior officers.

In fact, once news of Hall’s lawsuit surfaced, the soldier, who served two tours of duty in Iraq, returned to Fort Riley Army base in Kansas from Combat Operations Base Speicher because other soldiers allegedly threatened to physically harm him. The military determined that it could not protect Hall and in November 2007 sent him home.

When Hall returned to Fort Riley, his situation did not improve, Weinstein said.

It was during this time, the lawsuit alleges, that Hall was being considered for a promotion, which was withdrawn when Fort Riley Army officials discovered Hall had sued the Defense Department and was unwilling to set aside his atheist beliefs.

“The day following this media attention, the Commanding General of Fort Riley sent out a post-wide memo. This post-wide memo stated that plaintiff Hall was engaged in a lawsuit. Following the issuance of the memo on December 19, 2007, plaintiff Hall was notified that he would not be considered for promotion.

“When plaintiff Hall learned that he would be denied an appearance before the promotions board, he sought counseling from Sergeant Van Hise, who informed plaintiff Hall that since he was ‘under investigation,’ he was not eligible for an appearance before the promotions board. Sergeant Van Hise stated that plaintiff Hall was unable to put aside his personal convictions and pray with his troops.

“Sergeant Van Hise believed this to be a constraint on Army morale and would limit plaintiff Hall’s ability to bond with his troops. Plaintiff Hall responded that religion is not a requirement of leadership. At this, Sergeant Van Hise questioned how plaintiff Hall could ask for religious freedom when in fact, as an atheist, he has no religion. Plaintiff Hall replied that the United States Army Chaplain’s manual protects atheism,” the lawsuit states.

Still, the Justice Department, says the case should be dismissed, because Hall and his Speicher supervisor Maj. Welborn haven’t encountered one another since last summer and as a result Hall and MRFF “cannot establish that any injury allegedly caused Welborn is likely to recur in the future.”

Welborn has vehemently denied the charges Hall lodged against him.

Welborn has not returned calls for comment.

On his MySpace page he wrote that he is a devout Christian who received a bachelor’s degree in “personal evangelism” and a minor in “Biblical world view” from Temple Tennessee University. He said that he is pursuing a second bachelor’s degree in Christian studies from Calvary Bible College And Theological Seminary in Kansas City, Missouri. He lists his occupation as “Bible Study–Operation Iraqi Freedom” and wrote that his interest is evangelism and preaching the Gospel of Jesus Christ.

“Currently serving w/3rd Inf Div [3rd Infantry Division] Civil Military Operations (Governance) in Baghdad Iraq,” Welborn, who appears in his Army uniform wrote on his MySpace page. He described himself as a “Warrior for the Lord Jesus Christ.” He wrote that he and his wife Carla “place all our Faith & Trust in our Savior the Lord Jesus – who provides eternal life to anyone that believes that he is the Son of God, that he was born of a virgin, lived as God in the flesh (as man) was crucified, died, and was buried then rose from the grave the third day, then acended [sic] to the right hand of the Father – True repentance (turning away from Sin to God) Being born again, Forgivness [sic] & Justification occure [sic] to the True Believer in Christ when Baptized w/God’s Holy Spirit.”