But he believes his fight -- that triggered a provocative opinion from a federal district court judge -- has just begun.
"To millions of people, particularly African-Americans, the Confederate battle emblem is a symbol of Old Mississippi -- the Mississippi of slavery, lynchings, pain and white supremacy," wrote U.S. District Court Judge Carlton W. Reeves in an opinion on Thursday.
"The emblem offends more than just African-Americans," he added, "it is difficult to imagine how a symbol borne of the South's intention to maintain slavery can unite Mississippians in the 21st century."
While making clear his disdain for the flag, Reeves who was appointed to the bench by President Barack Obama in 2010, said he had to dismiss Moore's case on a procedural issue. Reeves said that Moore did not have the "standing," or legal right to be in court. Reeves held that Moore couldn't show a "cognizable legal injury" necessary to bring the case.
But the judge left open the possibility that another case could be brought or "the people themselves" could act to change the flag.
"Today, Mississippi stands alone," Reeves wrote, "it is the only state to include the notorious 'stars and bars' in its official flag."
"At times there is something noble in standing alone," Reeves continued. "This is not one of those times."
Moore said in an interview that he was disappointed that the judge blocked his case from going forward, and he plans to file an appeal this week with the Fifth Circuit Court of Appeals.
But he believes from a historical perspective the judge "hit the nail on the head."
"While he dismissed my lawsuit, he definitely left the door open and seemed to be receptive to others challenging the constitutionality of the state flag in the federal court, or to the voters themselves," he said.
Moore has also attention of a lawyer from a Philadelphia law firm.
"I think the judge did a remarkable job of exploring and laying out the historic context of which the flag arose, the way the flag has been used for a more than a century and laying out why it is wrong to have a state incorporate that emblem into its official state flag. However, the judge interpreted 'standing' in a way that is not consistent with Supreme Court precedent," said the new lawyer, Michael T. Scott of Reed, Smith.
Moore argues in court briefs that the flag is "tantamount to hateful government speech that both has a discriminatory intent and disparate impact and violates the Equal Protection Clause of the 14th Amendment."
The lawsuit targets Gov. Phil Bryant. Bryant was not required to answer Moore's allegations, but his office filed a motion to dismiss arguing that Moore's complaint is "devoid of a single allegation that he has personally suffered a concrete and particularized injury."
Lawyers for the state argued that while Moore may sincerely hold a belief that the flag "allegedly incites racial violence," such "generalized fear of future injury is insufficient to confer standing."
In court papers they stress that the Mississippi Supreme Court has weighed in on the issue and ruled that the decision to "fly or adopt" a state flag rests " entirely with the political branches."
Reeves' opinion walks through the flag and the state's history and discusses a case brought by the Mississippi State Conference of NAACP branches and individuals. In 2001, the Mississippi legislature set a special election where voters had the option of choosing an alternate design. According to Reeves, "the special election results substantially favored the 1894 flag."
In January 2016, several bills were introduced regarding the flag, but they did not clear committee hurdles.
Marc Allen, public affairs officer for the Mississippi Division of the Sons of Confederate Veterans, a group that says it works to honor the reputation of soldiers who fought for the confederacy during the Civil War says Reeves was right to dismiss the case, but he misrepresented the state's history.
"This is not a federal judge issue, this is an issue for the people of the State of Mississippi to decide," Allen said. Allen calls the emblem " a battle standard, it's what the confederate soldier looked to on the battlefield."
"I think the judge doesn't understand the history of what he is saying," Allen said. "A lot of people will point to its use by hate groups, but if you use that logic, we also have to get rid of the Christian cross and the bible."