Several Marines from Camp Pendleton are under investigation and the former squad leader, now a civilian, has been charged in federal court with two counts of voluntary manslaughter.
But getting charges to stick could prove difficult as prosecutors try to assemble concrete evidence from a battle that reduced much of the city to rubble and caused extensive casualties.
Over the course of the 53-day battle, about 130 Marines were killed, more than 1,000 were wounded and about 1,000 insurgents were killed, Marine spokesman Lt. Col. Chris Hughes said. There is no tally of civilian deaths.
"It's a little bit difficult to take a firefight three years after the fight and try to piece together whether or not a crime took place," said Doug Applegate, an attorney for Jose Nazario Jr., the former squad leader. "No crime scene could have been preserved, there's no physical evidence or DNA."
Nazario, 27, who has left the Marine Corps, pleaded not guilty earlier this month in federal court in Riverside.
Recent cases against Marines over actions in Iraq highlight the challenges prosecutors face. A case brought against eight members of a squad in the killing of an Iraqi man last year in Hamdania resulted in only one murder conviction, despite confessions and testimony from several of the defendants.
A year after the alleged shootings in Fallujah, a different squad was involved in the killings of 24 civilians in Haditha, but prosecutors have yet to score any convictions in the case.
Observers say it will be even tougher to prosecute the alleged killing of prisoners in Fallujah by members of a squad from Kilo Company, 3rd Battalion, 1st Marines.
There are no forensics, the building where the shootings supposedly took place was destroyed and the identity of the victims is unknown, lawyers for some of the squad members said.
Prosecutors have identified the men Nazario allegedly shot only as "human beings" called John Doe No. 1 and John Doe No. 2.
Already, the officer overseeing the case has dismissed a murder charge against one squad member, Sgt. Jermaine Nelson. Lt. Gen. James Mattis could still decide to charge Nelson, but in the Hamdania and Haditha cases he showed a tendency to give troops the benefit of the doubt.
"It's a very difficult case," said Gary Solis, a former Marine Corps prosecutor and judge who teaches law of war at Georgetown University Law Center. "I'm sure glad that I don't have to do it."
The investigation was triggered by a former corporal from the squad, Ryan Weemer, in the process of applying for a job with the Secret Service. Investigators claim Weemer described the killings during a polygraph test that included a question about whether he had participated in a wrongful death, according to his attorney, Paul Hackett. Weemer has not been charged with any crime.
Nazario's criminal complaint states the squad had been taking fire from a house in Fallujah. After the troops entered the building and captured several insurgents, Nazario placed a call on his radio.
"Nazario said that he was asked, 'Are they dead yet?"' the complaint states. When Nazario responded that the captives were alive, he was told by the Marine on the radio to "make it happen," the complaint says.
Thad Coakley, a major in the Marine reserves and a former Camp Pendleton prosecutor, said Nazario's case is more likely to go to trial than it would in military court. That's because federal prosecutors presented evidence to a secret grand jury with no rebuttal from the defense. In the military system, a defendant can challenge evidence at a hearing to determine if there will be a trial.
Lawyers say it is highly unusual for civilian prosecutors to go after a former U.S. serviceman for an alleged war crime. Kevin McDermott, another of Nazario's lawyers, said prosecutors pursued charges by employing a little-used 2000 law written primarily to prosecute civilian contractors who commit crimes while working for the U.S. overseas.
McDermott said he knew of only one other veteran, former Army Pvt. Steven Green, to be charged in civilian court. Green is accused of raping and murdering a 14-year-old Iraqi girl, then killing members of her family. He faces a possible death sentence when he is tried in federal court in Kentucky.
Still, Coakley said, winning a conviction in either forum would be difficult. "It's almost impossible in my opinion to prove anything (in this case) beyond a reasonable doubt," he said.
If Nazario's case goes to trial, Applegate said he would educate a civilian jury about the realities of combat.
"How do you convey to a jury confusion in the fog of war?" Applegate said. "We are going to have to convey that a guy who might cross the street under a white flag on your block might shoot your best friend on the next block."
The battle of Fallujah in fall 2004 is ingrained in Marine Corps legend. It was the second time that year Marines tried to take the city. The first fight in April 2004 came after the killing and mutilation of four Blackwater private security contractors, whose bodies were strung from a bridge.
Marine, Army and Iraqi units assembled for a second assault and on Nov. 7, 2004, after weeks of propaganda efforts to make civilians leave, an intense bombardment began.
Ground forces entered Fallujah on Nov. 9 and faced some of the heaviest fighting seen so far in the war in Iraq, often engaging in hand-to-hand combat.
"It was brutal, brutal warfare," said author Nat Helms, who spoke to more than 100 Marines for a book about the battle.
Members of Nazario's squad are alleged to have shot the captured insurgents on the morning of Nov. 9, about 30 minutes after losing a comrade to sniper fire, Helms said.
His book, "My Men Are My Heroes: The Brad Kasal Story," is named after a Marine sergeant who was praised for his actions in a different firefight in Fallujah. Helms said many Marines acted heroically.
"If you want to blame people for conduct in this war, blame those that started it," Helms said. "Don't blame them for being warriors."
Of more than 20 Navy Cross medals awarded for combat heroism in Iraq and Afghanistan, at least eight were earned in Fallujah, according to several online sources. A Navy Cross is second only to a Medal of Honor.
Weemer's attorney, Hackett, a Marine reservist major, saw firsthand the destruction unleashed on Fallujah and said almost every building was badly damaged.
Hackett said it is unlikely someone who has never seen combat could grasp what Marines experienced there.
"I remember the first day seeing a dog run down the street with an arm in its mouth. Dogs, cats eating bodies. Those are the kinds of scenes that a Marine is experiencing," Hackett said.
"You take a 22-year-old American, you shoot at him all day long, you deprive him of sleep, you make him see his buddies being killed, he has their blood on his boots and blouse, and when you don't see perfection in his decisions you court-martial him? It's absurd."