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General Thomas Lawson, right, Chief of the Defence Staff , returns a salute to Major General Dean Milner, last Commander of the Canadian Contribution to the Training Mission in Afghanistan, during the flag-lowering ceremony at the International Security Assistance Force (ISAF) headquarters in Kabul on March 12, 2014. The ceremony marked the end of Canada's 12-year military involvement in Afghanistan.HANDOUT/Reuters

It's over – again. The Maple Leaf flag came down in Kabul on Wednesday, marking the end of Canada's 12 years of military involvement in Afghanistan.

The final three-year training mission, the last task of Canadian soldiers, was always a coda – reluctantly accepted by Prime Minister Stephen Harper's government as a kind of after-mission in a war it wanted to leave.

But like the departure of Canadian combat troops from Kandahar in 2011, this mission's conclusion leaves things unfinished. The task was to build up Afghanistan's army, but it remains far short of a standalone force. The numbers have grown and Afghan soldiers have better infantry training, but there are still problems: heavy desertion, a lack of logistics and air capabilities, and, according to a recent report, many soldiers remain illiterate.

Wednesday's ceremony marked a kind of second end. The bloodier sacrifices of combat in Kandahar, with 158 soldiers and one diplomat dead, created controversy and grief at home. When the combat ended, attention waned, even though 900 trainers were still in the country.

"It's a different feel," said Major-General Dean Milner, who was the last commander of Canadian combat troops in Kandahar in 2011, and is now the last commander of the training mission. "When we left Kandahar, that was more war fighting. This one's been focused on training the Afghan soldier."

It's understandable that the combat mission garnered more attention, Maj.-Gen. Milner said in a interview from Kabul on Wednesday. "But the shift up here has had strategic impact."

Like most things connected to Canada's role in Afghanistan, the successes of the training mission are mixed, and the impact will be measured over time. The basic strategy behind training was clear: It was part of an exit strategy for Canada.

In 2010, Mr. Harper had made up his mind to leave Afghanistan, and had made a pact with the opposition to do it. He had little hope left that the Afghan government of President Hamid Karzai was going to establish an effective government across the country. There was little appetite to extend the Canadian presence. "We were done," one former official said.

But allies pressed Canada to continue some involvement. U.S. President Barack Obama spoke to Mr. Harper on the margins of the G20 summit in Toronto about some kind of continuing Canadian role – and Mr. Harper quietly dispatched his then foreign minister, Lawrence Cannon, to meet U.S. Secretary of State Hillary Clinton to discuss it. The details of the Canadian training mission were hammered out between Ottawa and Washington.

Politically, however, the training mission wasn't allowed to get in the way of the main message: Canada's commitment in Afghanistan was winding down. After combat troops left Kandahar, the government said little about the continuing role. The federal government website on Afghanistan still features headlines that haven't been updated since 2012.

It's perhaps not surprising: Canadians were war weary. The government points to more Afghan students in schools, and fewer safe havens for al-Qaeda terrorists, to declare the job done.

But despite the perennially positive reports from Canadian military commanders and government, the Canadian mission in Afghanistan was not a success, said Roland Paris, of the University of Ottawa's Graduate School of Public and International Affairs. Canadian soldiers did good work, but tactical gains made in Kandahar were soon undone by insurgents, he said; widespread security and stability were not achieved. And it remains unclear what will happen when most international forces leave at the end of this year.

The training of the Afghan National Security Forces – the army and police – is critical to that outcome. After years of Western combat troops fighting insurgents, the NATO training mission, in which Canadians played a major role, is key to what happens after foreign troops leave. Numbers in the Afghan army and police have increased by about 100,000 in four years, and Maj.-Gen. Milner said they're nearly ready.

"They're pretty darn close now. They're about 350,000, and they're confident and capable," he said.

When Canadian trainers first arrived three years ago, they were helping to build Afghan units known as kandaks, advising Afghans on providing "basic warrior training," and then establishing schools for infantry and engineers – "training the trainers" by teaching Afghan instructors, Maj.-Gen. Milner said. Afghan National Army troops showed they are capable fighters when they took over the "lead" role in combat operations last year.

He conceded, however, that challenges remain: Attrition remains a concern, with some reports suggesting one-third of Afghan troops desert. And while Afghan troops can fight, the country needs to build up the capacity to supply them and maintain equipment, Maj-Gen. Milner said.

"We've still got a lot more work to do," he said.

Recent independent assessments have been more critical. One audit found that the NATO training mission's effort to provide literacy training to all recruits has become a mess.

An assessment of Afghan forces by CNA Strategic Studies, commissioned by the U.S. Congress, found that they lack key logistics and air-support capabilities, so they will still need international military help after 2014. And, critically, the assessment concluded NATO's plan that the numbers of Afghan troops and police can be reduced to 228,000 – to reduce the cost – is faulty. It's not clear if the Afghan forces will be able to hold off insurgents in the country's east and south.

But Canada's mission is over. The flag has been lowered at NATO's Kabul headquarters for the last time, leaving trainees to carry on Afghanistan's war.

Campbell Clark is The Globe's chief political writer.