An Army specialist who served two tours of duty in Iraq sued Defense Secretary Robert Gates and his supervising officer Wednesday for allegedly trying to force him to embrace fundamentalist Christianity and then retaliating against him when he refused.

Plaintiffs Jeremy Hall, who was stationed at Combat Operations Base Speicher, Iraq, and the Military Religious Freedom Foundation (MRFF) filed the lawsuit in US District Court in Kansas City, Kansas, Wednesday afternoon. The complaint was originally filed last year but withdrawn a month ago in order to include new allegations that says Hall's promotion in the Army was withdrawn because of his pending lawsuit against the military.

The complaint alleges that Hall's First Amendment rights were violated as early as Thanksgiving 2006 when, because of his atheist beliefs, Hall declined to participate in a Christian prayer ceremony commemorating the holiday.

"Immediately after plaintiff made it known he would decline to join hands and pray, he was confronted, in the presence of other military personnel, by the senior ranking . . . staff sergeant who asked plaintiff why he did not want to pray, whereupon plaintiff explained because he is an atheist," the lawsuit states. "The staff sergeant asked plaintiff what an atheist is and plaintiff responded it meant that he (plaintiff) did not believe in God. This response caused the staff sergeant to tell plaintiff that he would have to sit elsewhere for the Thanksgiving dinner. Nonetheless, plaintiff sat at the table in silence and finished his meal."

Additionally, the complaint alleges that last July, when Hall received permission by an Army chaplain to organize a meeting of other soldiers who shared his atheist beliefs, his supervisor, Army Major Freddy Welborn, broke up the gathering and threatened to retaliate against the soldier by charging him with violating the Uniform Code of Military Justice. The complaint also alleges that Welborn vowed to block Hall's reenlistment in the Army if the atheist group continued to meet -- a violation of Hall's First Amendment rights under the Constitution.

"During the course of the meeting, defendant Wellborn confronted the attendees, disrupted the meeting and interfered with plaintiff Hall's and the other attendees' rights to discuss topics of their interests," the lawsuit alleges.

The complaint charges that Hall, who is based at Fort Riley, Kansas, has been forced to "submit to a religious test as a qualification to his post as a soldier in the United States Army," a violation of Article VI, Clause 3 of the Constitution.

A Pentagon spokesman said he could not comment on the lawsuit because he has not yet seen it.

The amended lawsuit claims that a pattern of anti-Islamic sentiment exists in the military as demonstrated by photographs Hall took of posters at the Fort Riley Army base in December featuring conservative commentator and author Ann Coulter that included a statement she made several years ago about executing the leaders of Islamic nations and converting their citizens to Christianity.

Hall sent the images to representatives for MRFF and some were distributed to the media, which published stories about the issue. It was during this time, the complaint alleges, that the promotion Hall was being considered for had been withdrawn because Army officials at Fort Riley 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," the lawsuit states. "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."

Mikey Weinstein, the founder and president of The Military Religious Freedom Foundation, in an interview, said, �It is beyond despicable, indeed wholly unlawful, that the United States Army is actively attempting to destroy the professional career of one of its decorated young fighting soldiers, with two completed combat tours in Iraq, simply because he had the rare courage to stand up for his constitutional rights and guarantees of separation of church and state against a superior officer who was forcefully attempting to intimidate him into accepting fundamentalist Christianity."

"Our new federal lawsuit will show the almost incomprehensible national security risks to America and the world as a result of the destruction of the wall separating Church and State in the United States armed forces,� he added. �The United States military is actively engaged in a pernicious and pervasive pattern and practice of unconstitutional rape of the precious religious freedoms of our honorable and noble sailors, soldiers, airmen, marines, National Guard, reservists and veterans. This evil is a noxious, institutional force-feeding of fundamentalist Christianity by our nation's military command structure in complete defiance of the United States Constitution."

Weinstein, a former White House attorney under Ronald Reagan, general counsel H. Ross Perot and an Air Force Judge Advocate (JAG), has been waging a one-man war against the Department of Defense for its blatant disregard of the Constitution. He published a book on his fight: "With God on Our Side: One Man's War Against an Evangelical Coup in America's Military." Weinstein is also an Air Force veteran and a graduate of the Air Force Academy. Three generations of his family have attended US military academies.

Since he launched his watchdog organization more than three years ago, Weinstein said he has been contacted by more than 6,000 active duty and retired soldiers, many of whom served or serve in Iraq, claiming that they were pressured by their commanding officers to convert to Christianity.

In August, the Pentagon's inspector general responded to a complaint filed in 2006 by Weinstein�s organization alleging that Defense Department officials violated military regulations by appearing in a video promoting a fundamental Christian organization.

The inspector general agreed and issued a 47-page report that was highly critical of senior Army and Air Force personnel for participating in the video while in uniform and on active duty.

The 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 in the inspector general's report, "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."

Hall�s decision to become a plaintiff with MRFF in a lawsuit against the Pentagon has had repercussions. Last September, while Hall was still stationed in Iraq, he said other US soldiers physically threatened him after word spread that he and MRFF sued the Pentagon and the secretary of defense. On popular military related blogs, such as military.com, individuals who claimed they were active-duty soldiers posted comments threatening Hall with "fragging," a term used by the military in which an unpopular soldier could be killed by intentional friendly fire during combat. The comment received widespread attention on blogs and in November Hall was transferred from Combat Operations Base Speicher to Fort Riley, Kansas.