The recently retired commandant of the Marine Corps and a three-star general remain at odds over the handling of a scandal that bruised the commandant’s reputation and led to allegations of abuse of power, according to the results of a Defense Department inspector general report obtained by The Washington Post.

Pentagon investigators cleared Commandant Gen. James F. Amos of allegations that he attempted to pressure Lt. Gen. Thomas Waldhauser for a tougher outcome in the handling of legal cases stemming from a viral video that was recorded in 2011 and that depicted Marine snipers urinating on dead Taliban fighters in Afghanistan. Waldhauser was the top officer overseeing the cases at the time, meaning that any interference by Amos would have raised the prospect of unlawful command influence, in which a senior officer seeks to push a junior commander for a certain outcome in a case.

The inspector general cleared Amos of wrongdoing in July, but defense officials declined at the time to release the related report. The documents obtained by The Post indicate that, although the allegations against the commandant were not substantiated, senior officers involved in the handling of the cases do not see eye-to-eye on all that occurred.

Public affairs officers for Amos and the Joint Staff, where Waldhauser works now, declined to comment.

Pentagon investigators said they could not determine whether Amos had told Waldhauser that he wanted the Marines involved “crushed,” as Waldhauser alleged  in a July 2013 court filing first publicized by the independent Marine Corps Times.

Waldhauser was stripped of his responsibility as the legal convening authority in the cases after discussing them with Amos in the United Arab Emirates on Feb. 6 and Feb. 7 in 2012, both men told investigators. But their stories diverge there.

According to the inspector general’s report, Waldhauser said that he sent Amos an e-mail on Jan. 31, 2012, believing that he had sufficient information to initiate punishment against the four Marines who appeared in the video and a fifth who recorded it. He wanted the commandant’s guidance on the “pacing” of the proceeding against those involved, he said.

The commandant and Waldhauser met in the UAE on Feb. 6 and had dinner with a number of Marine Corps generals and other officials. At some point during that meal, Amos made his displeasure with the snipers clear, Waldhauser told the IG.

“I remember it like it was yesterday,” Waldhauser told investigators, the IG documents say. “… the Commandant leaned back in his chair, looked at me right in the eye very close and said, ‘Those guys need to be crushed.’ ”

The conversation turned to other subjects, but the following day Waldhauser and the commandant discussed the cases again for about 30 minutes in a private jet terminal, Waldhauser said. Amos asked him if he was going to bring them to a general court-martial, which could have resulted in serious consequences for those involved.

Waldhauser’s preferred plan at the time is redacted from the report, but it has been reported previously that he intended to subject at least some of the Marines involved to  nonjudicial punishment. Amos told the inspector general that he was “incredulous” with Waldhauser’s plan and noted that it was still receiving heavy media coverage, including in the Middle East.

“I tried to convey my seriousness to what the hell is going on here, and he sees it only from the Component Commander’s perspective, the Commander of Marine Forces Central Command, the Commander of 1st Marine Expeditionary Force at Camp Pendleton,” Amos told the inspector general, rattling off Waldhauser’s jobs at the time. The commandant added that he was looking at it “from Service chief, Washington D.C., President of the United States, global TV, Secretary of the Defense, Secretary of State, Congress.”

“… I’m trying to convey that this is really, really serious,” Amos told investigators, according to the documents. “… So when I lean in, I’m trying to convey, ‘Tom, this is serious s—.”

Both men agreed in their testimony that their conversation remained professional. But Amos said he did not recall that he ever said he wanted the Marines crushed. In an interview with NPR in February, he was more emphatic, saying he “never, ever said that I wanted them crushed and kicked out.” Amos said that him doing so at a dinner, rather than in a professional setting, also wouldn’t have been his way of doing business.

The two generals parted ways, and Amos decided within 24 hours to remove Waldhauser as the general in charge of the cases. He did so, he said, because he did not want his conversation with the three-star general to be misconstrued as having put pressure on him.

Waldhauser, asked by investigators whether he thought he was removed from the cases because his judgment was being questioned, shifted focus to Amos’s decision.

“The Commandant said, ‘My remarks could have caused a problem,’ ” Waldhauser said, according to documents obtained by The Post. “The Commandant said, ‘I need to fix this.’ That’s why I was removed.”

The inspector general found that, even if Amos had said he wanted the snipers “crushed,” the remark alone would not have constituted unlawful command influence. Investigators pointed to Amos’s decision to replace Waldhauser with another senior officer, Lt. Gen. Richard Mills, as evidence of his “intent to ensure that the disciplinary process was untainted by inappropriate influence.”

The documents were provided by Lee Thweatt, a former Marine officer and frequent critic of Amos’s who had filed suit to obtain them. (The Post also sought the documents through a Freedom of Information Act request.) Their existence was confirmed by defense officials.

Thweatt said he believes the report “whitewashes” what happened and does not address that the government conceded in the court cases that Amos appeared to commit unlawful command influence.

Eight Marines faced discipline as a result of the cases. None faced general court-martial or confinement. Most reached plea agreements, although charges were dropped against the one officer implicated, Capt. Matthew Clement. He was not accused of participating in the video, but an administrative board of Marine officers found that he did not properly supervise the snipers involved. He was forced out of the Marine Corps with an honorable discharge.

The inspector general report notes that investigators did not address the question of whether any of the Marines charged should be able to seek legal redress as a result of their findings. A spokesperson for the inspector general, Bridget Serchak, declined to comment further.

A spokesman for the Defense Department on the issue could not be reached for comment on Tuesday.