The Afghanistan war crimes allegations have been under investigation for four years, but the scope, reasons and depth of depravity were new to anyone not linked to the inquiry.

Special forces have been on tenterhooks, worried about what might come out, worried about the legacy of their service, worried that any minor breakdown of good discipline would have them tarred with the same brush as those involved in murder.

Now we know that 25 Australian soldiers, out of hundreds involved in special operations in Afghanistan, have been linked to the alleged murder of 39 Afghan individuals, including children, and 19 soldiers will likely face the most grave charges.

Everyone else has been sentenced to soul-searching.

Defence Force Chief General Angus Campbell opened up about his own soul-searching this week when he released the report.

"No, I didn't see these things, and I'm wondering what I did miss, and what could have been done otherwise," he said.

"Our reputation, how we're treated, that's about each day and the performance we give each day as we move forward.

"Whenever there was an allegation of an incident there must have been someone in the vicinity of that incident. I want there to be a path for them to say it, and [to make sure] that they're heard."

Since then soldiers have liberally shared a quote from American investor Warren Buffett: "It takes 20 years to build a reputation and five minutes to ruin it. If you think about that, you'll do things differently."

Senator Linda Reynolds wears two hats in this situation, that of Minister for Defence and that of a former serving member herself.

"It made me feel very ill," she said about reading the final report two weeks ago.

"Very distressing. It doesn't represent my service ... or the majority of our men and women who have served our nation in uniform."

Prime Minister Scott Morrison has announced an Office of the Special Investigator and an oversight committee to handle the next steps. He has apologised to the people of Afghanistan, an apology that was later echoed by General Campbell.

Two former prime ministers have also weighed in. John Howard, as the PM who committed Australian forces to Afghanistan in 2001, said he felt distress at the conduct, which he said was totally at odds with the values of the ADF, but he remains intensely proud of the bravery and professionalism of those forces in the years that followed.

"A long road lies ahead," he said of the prosecutions. "In the meantime, we should remember the continuing service of our military personnel and, where appropriate, extend a helping hand to them and their families."

Kevin Rudd, who was prime minister during part of the period covered by the investigation, said he was "utterly disgusted" by the accounts, and joined in Scott Morrison's apology to the people of Afghanistan.

"Behind every unlawful killing is a family grieving for someone they love," he said. "The Chief of the Defence Force now has an urgent responsibility to reform the culture of these units and ... align military culture and practices with the expectations of the Australian people ... to mend our country's reputation."

Brendan Nelson, both a former defence minister and former director of the Australian War Memorial, has been a strident defender of the reputation of the special forces. In 2018 he asked "where lies the national interest in tearing down our heroes?"

"War is a very messy business," he told Sky News at the time. "Within a tight-knit group of people, in this case the SAS, our commandos, there are different recollections of adrenaline-charged incidents that occur in war." He declined to comment this week.

In interviewing former senior leaders and veterans of other ranks this week, it is clear there is a profound sadness, as well as anger that some special forces have allowed their media substitutes to propagate a "fog of war" defence when Justice Brereton found that was not the case in the alleged premeditated murders. They have spoken of a decline in ethics in parts of the service over decades, and of not recognising the actions of the men in these reports.

One former admiral noted that Robert Graves' memoir Goodbye to All That retells a story of an Australian killing prisoners, and how on the Western Front it was initially the Canadians that had the worst reputation, and then it was the Australians. We've been here before.

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Can you train ethics? General Campbell made it a priority in his statement this week.

The Centre for Defence Leadership and Ethics sits within the Australian Defence College. Its commander, Major-General Mick Ryan, says they run simulations to prepare ADF leaders to deal with these issues, both when the pressure is on and when they have time to think through their actions.

"We prepare our leaders, enlisted and officers to make decisions that aren't just in accordance with the laws of our country, but are in accordance with the values and expectations of the people in our country," General Ryan said.

Using people with a record of being ethical leaders, including former sergeants and former senior officers, they've found their case studies very powerful because they allow people to put themselves in the position of someone who's had to make decisions under very difficult circumstances - sometimes in the heat of battle, sometimes not in battle.

General Ryan said they cover acting unethically, doing things that aren't legal, unlawful killing, injuring damage to property and religious sites, as well as laws of armed conflict preparation. The training has been running for 20 years - longer than Australia's involvement in Afghanistan.

Lessons from the Brereton report are already being incorporated and will be ready from January 1.

He too is soul-searching: "I felt heartsick that we had engaged in such repulsive behavior that we had let down those in Afghanistan we were there to help, that we had let down our army and that we, as military professionals, had let down the society that trusts us."