Now known as Academi, the company was sold by its founder, Erik Prince, to a group of private investors three years after the Nisour Square killings.

But the difficulty the government has had in making a case against the former employees is likely only to reinforce the impression that American contractors were not subject to any rules in Iraq, despite the Obama administration’s attempts to allay Iraqi concerns about the case and Vice President Joseph R. Biden Jr.’s expression of his “personal regret” for the shooting.

Image Nicholas A. Slatten, a contractor, in 2008. Accused of firing the first shots, he faces a new charge of first-degree murder. Credit... Douglas C. Pizac/Associated Press

“As citizens, we need to ask why our government fails to achieve any accountability for such blatant wrongdoing,” said Susan Burke, a lawyer who represented Iraqi victims of the Nisour Square shooting in a lawsuit that Blackwater settled by paying an undisclosed amount. “The ongoing delays and mistakes undermine any confidence in the system.”

When the F.B.I. team arrived home from Iraq in 2007, court testimony and interviews show, members believed they had the makings of a strong case. Witnesses told a horrific tale, and while Blackwater guards said the shooting had begun with an ambush by insurgents, American military officials told investigators that there had been no sign of such an attack. Even if there had been, the military said, firing grenade launchers in such a crowded space was excessive.

“It was an investigation into the protection of basic human rights that should be afforded to all people, not just citizens of the United States,” Joseph Persichini Jr., the assistant F.B.I. director then in charge of the Washington field office, said in 2008.

But from the beginning, investigators said, they felt their case was being undermined. A State Department security agent reported that, shortly after the shooting, his colleagues had gathered up shell casings, trying to clean up the scene to protect Blackwater. The agent, David Farrington, recalled a meeting in which other State Department officials said, “We’ve got enough to get these guys off now,” according to court testimony.