The brother-in-law of VS Naipaul, the British novelist and Nobel laureate, was murdered last month after threatening to expose Pakistani army generals who had made deals with Taliban militants.

Major-General Faisal Alavi, a former head of Pakistan’s special forces, whose sister Nadira is Lady Naipaul, named two generals in a letter to the head of the army. He warned that he would “furnish all relevant proof”.

Aware that he was risking his life, he gave a copy to me and asked me to publish it if he was killed. Soon afterwards he told me that he had received no reply.

“It hasn’t worked,” he said. “They’ll shoot me.”

Four days later, he was driving through Islamabad when his car was halted by another vehicle. At least two gunmen opened fire from either side, shooting him eight times. His driver was also killed.

This weekend, as demands grew for a full investigation into Alavi’s murder on November 18, Lady Naipaul described her brother as “a soldier to his toes”. She said: “He was an honourable man and the world was a better place when he was in it.”

It was in Talkingfish, his favourite Islamabad restaurant, that the general handed me his letter two months ago. “Read this,” he said.

Alavi had been his usual flamboyant self until that moment, smoking half a dozen cigarettes as he rattled off jokes and gossip and fielded calls on two mobile phones.

Three years earlier this feted general, who was highly regarded by the SAS, had been mysteriously sacked as head of its Pakistani equivalent, the Special Services Group, for “conduct unbecoming”. The letter, addressed to General Ashfaq Kayani, the chief of army staff, was a final attempt to have his honour restored.

Alavi believed he had been forced out because he was openly critical of deals that senior generals had done with the Taliban. He disparaged them for their failure to fight the war on terror wholeheartedly and for allowing Taliban forces based in Pakistan to operate with impunity against British and other Nato troops across the border in Afghanistan.

Alavi, who had dual British and Pakistani nationality, named the generals he accused. He told Kayani that the men had cooked up a “mischievous and deceitful plot” to have him sacked because they knew he would expose them.

“The entire purpose of this plot by these general officers was to hide their own involvement in a matter they knew I was privy to,” he wrote. He wanted an inquiry, at which “I will furnish all relevant proof/ information, which is readily available with me”.

I folded up the letter and handed it back to him. “Don’t send it,” I said. He replied that he had known I would talk him out of it so he had sent it already. “But”, he added, “I want you to keep this and publish it if anything happens to me.”

I told him he was a fool to have sent the letter: it would force his enemies into a corner. He said he had to act and could not leave it any longer: “I want justice. And I want my honour restored. And you know what? I [don’t] give a damn what they do to me now. They did their worst three years ago.”

We agreed soon afterwards that it would be prudent for him to avoid mountain roads and driving late at night. He knew the letter might prove to be his death warrant.

Four days after I last saw him, I was in South Waziristan, a region bordering Afghanistan, to see a unit from the Punjab Regiment. It was early evening when I returned to divisional headquarters and switched on the television. It took me a moment to absorb the horror of the breaking news running across the screen: “Retired Major General Faisal Alavi and driver shot dead on way to work.”

The reports blamed militants, although the gunmen used 9mm pistols, a standard army issue, and the killings were far more clinical than a normal militant attack.

The scene at the army graveyard in Rawalpindi a few days after that was grim. Soldiers had come from all over the country to bury the general with military honours. Their grief was palpable. Wreaths were laid on behalf of Kayani and most of the country’s military leadership.

Friends and family members were taken aback to be told by serving and retired officers alike that “this was not the militants; this was the army”. A great many people believed the general had been murdered to shut him up.

I first met Alavi in April 2005 at the Pakistan special forces’ mountain home at Cherat, in the North West Frontier Province, while working on a book about the Pakistani army.

He told me he had been born British in Kenya, and that his older brother had fought against the Mau Mau. His affection for Britain was touching and his patriotism striking.

In August 2005 he was visiting Hereford, the home of the SAS, keen to revive the SSG’s relationship with British special forces and deeply unhappy about the way some elements of Pakistan’s army were behaving.

He told me how one general had done an astonishing deal with Baitullah Mehsud, the 35-year-old Taliban leader, now seen by many analysts as an even greater terrorist threat than Osama Bin Laden.

Mehsud, the main suspect in the assassination of Benazir Bhutto late last year, is also believed to have been behind a plot to bomb transport networks in several European countries including Britain, which came to light earlier this year when 14 alleged conspirators were arrested in Barcelona.

Yet, according to Alavi, a senior Pakistani general came to an arrangement with Mehsud “whereby – in return for a large sum of money – Mehsud’s 3,000 armed fighters would not attack the army”.

The two senior generals named in Alavi’s letter to Kayani were in effect complicit in giving the militants free rein in return for refraining from attacks on the Pakistani army, he said. At Hereford, Alavi was brutally frank about the situation, said the commanding officer of the SAS at that time.

“Alavi was a straight-talking soldier and some pretty robust conversations took place in the mess,” he said. “He wanted kit, skills and training from the UK. But he was asked, pretty bluntly, why the Pakistani army should be given all this help if nothing came of it in terms of getting the Al-Qaeda leadership.”

Alavi’s response was typically candid, the SAS commander said: “He knew that Pakistan was not pulling its weight in the war on terror.”

It seemed to Alavi that, with the SAS on his side, he might win the battle, but he was about to lose everything. His enemies were weaving a Byzantine plot, using an affair with a divorced Pakistani woman to discredit him.

Challenged on the issue, Alavi made a remark considered disrespectful to General Pervez Musharraf, then the president. His enemies playeda recording of it to Musharraf and Alavi was instantly sacked.

His efforts to clear his name began with a request that he be awarded the Crescent of Excellence, a medal he would have been given had he not been dismissed. Only after this was denied did he write the letter that appears to many to have sealed his fate.

It was an action that the SAS chief understands: “Every soldier, in the moment before death, craves to be recognised. It seems reasonable to me that he staked everything on his honour. The idea that it is better to be dead than dishonoured does run deep in soldiers.”

Alavi’s loyalty to Musharraf never faltered. Until his dying day he wanted his old boss to understand that. He also trusted Kayani implicitly, believing him to be a straight and honourable officer.

If investigations eventually prove that Alavi was murdered at the behest of those he feared within the military, it may prove a fatal blow to the integrity of the army he loved.

Britain and the United States need to know where Pakistan stands. Will its army and intelligence agencies ever be dependable partners in the war against men such as Mehsud?

James Arbuthnot, chairman of the defence select committee, and Lord Guthrie, former chief of the defence staff, were among those who expressed support this weekend for British help to be offered in the murder investigation.

Inside the Pakistan Army by Carey Schofield will be published next year by Soap Box Books.

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