All over the country, there are offices, schools, workshops, banks, pharmacies, IT departments and factories where the failure of a colleague to arrive at work and thus miss a scheduled meeting would arouse some immediate questions. Such as: "Where is he?"

But not at MI6, apparently. When Gareth Williams didn't turn up at the office on 16 August 2010, there was not so much, initially, as an attempt to track him down, an inquiry of his family, or even a casual: "Strange, not like old Gareth to go Awol."

Instead, within the Vauxhall Cross headquarters of these guardians of national security, there was a bewildering lack of curiosity about the whereabouts of this super-fit, "world-class" code-breaking mathematician who had been seconded to the service from GCHQ, Cheltenham, had just completed a course enabling him to carry out covert operations, was hardly ever late, never had a day off sick, and had a journey to work that was but 1.7 miles.

Life at MI6 went seamlessly on. Mr Williams's line manager, known as "G" when he gave evidence at the inquest last week, merely "had a gut feeling that he was away doing something I was unaware of" – an explanation which suggests absenteeism in the service might be somewhat higher than is generally realised. "G" did try his phone, and also later went round to Williams's flat to give a tentative ring on his doorbell. But one, two, three, four, five, six days went by before, finally, on the seventh, the official alarm was raised.

That day, police entered his flat, and there in the bathroom, they found a large, red, zipped and padlocked North Face sports bag. And inside it was a very dead Gareth Williams. He had probably been there at least a week, the last known sighting of him being on the CCTV of Harrods on the day before he was due back at work.

This mysterious delay in taking any concerted action – and thus the non-discovery of his body for fully seven days – continues to trouble his family greatly, and has proved crucial. Williams had lain, in a bathroom and inside a plastic bag, for a week in August. By the time he was found, his body had significantly decomposed, as had any reliable forensic evidence. If he was drugged or poisoned, we shall never know. One of his superiors, deploying a nice line in understatement as she gave evidence behind a screen, conceded: "I appreciate the delay had some impact on the police investigation."

Mystery number two is how did he get there? Despite an apparent passing interest (if web searches are anything to go by) in bondage and the sexual thrills of being in a confined space, it seems inconceivable he could have placed himself in the bag, then zipped and locked it unaided. Police gave evidence to this effect, as did two experts in Houdini-like matters who have tried a total of 400 times to replicate such a manoeuvre. Fit and supple young men of the same build as Mr Williams – a keen cyclist and climber – could get into the bag, but could not find a way of closing the zip.

Small specks of another person's DNA have been found on the bag, adding to the obvious conclusion by police that Gareth had an assistant – or an assassin. It also seems likely that he was dead or unconscious before he went into the bag. The coroner's court heard from Detective Chief Inspector Jackie Sebire that he was in the foetal position, and there was no sign that he had scrabbled to get out. She said: "In my opinion he was very calm. His face was very calm. His hands were resting on his chest." There was no damage to the bag or his fingernails.

What on earth, then, went on inside the flat at the security services safe house at 36 Alderney Street, Pimlico, south-west London? The evidence suggests that, however upsetting it may be for his family, Mr Williams was a man of unusual tastes and habits. There were, in his apartment, female wigs, 26 shoes by designers including Stella McCartney and Christian Dior, a quantity of cosmetics and, in his bedroom, some £20,000 worth of designer women's clothes.

He was a frequent visitor to couture websites, and, the inquest heard, a regular browser and sometime purchaser at Dover Street Market – an edgy emporium in west London which carries a large range of designer clothes. Carol Kirton, who works there, said he regularly shopped in the store, saying the items were for his girlfriend.

This extensive and costly wardrobe was raised in court with a female friend, Sian Jones. She told the inquest she did not think he was a transvestite. "I feel he would have been able to confide in me ... and I would not have judged him." She said she saw him every few days and he "showered" her with gifts. Another friend, Elizabeth Guthrie, suggested the clothes might have been "Gareth's attempt at a support strategy for someone. They certainly would not have been for him".

The wigs were kept neat in netting; none of the cosmetics had been used, and many of the clothes – and they were of varying sizes, the inquest heard – were kept pristine in tissue. They may indeed have been a store of gifts for as-yet unidentified girlfriends, but there could be another interpretation. After all, if the hoard was not the collection of a fetishist, it was a very good imitation of it.

Could this be connected to his death? The bathroom was evidently a venue for at least one sexual climax for Mr Williams, traces of his semen were found on its floor. Did he have some companion in sexual, or pseudo-sexual, meanderings which involved being put into a confined space such as a sports bag?

This would not have been the first time some bedroom escapade had gone wrong. When he was working at GCHQ his home was in an annex let out by a Mr and Mrs Elliot, who lived in the adjoining house. One night, the couple heard Gareth's cries for help, and went to investigate. "We went upstairs and found him lying on the bed with both hands tied with material attached to the headboard," said Jennifer Elliot's written statement. She said that he explained how he had tied himself up as an experiment, but she wrote that she and her husband thought it "more likely to be sexual than escapology".

Mr Williams's career and its particular path are clearly a complicating context to the mystery of a brilliant man who served his country. His sister, Ceri Subbe, told the inquest: "He disliked office culture, post-work drinks, flash car competitions and the rat race. He even spoke of friction in the office. The job was not quite what he expected. He encountered more red tape than he was comfortable with."

Six months before his death he had completed an intensive course which would allow him to undertake what were described to the court as very tough operational tasks. But, according to his boss, he had applied for his three-year secondment at MI6 to be cut short – a request that was granted. There are also the unauthorised searches he made of security service databases about which the inquest heard. This was not, it seems, a settled man.

Neither police nor security services say they have reason to believe that his death was connected to his work for MI6. And, if any practitioner of "the dark arts" – as the lawyer for his understandably still-distressed family put it – wanted to kill him, surely it would have been a road "accident" while he was out cycling, an assignation on a bridge that would have ended with him "falling" into the Thames, or a simple bullet to the head? But not a modus operandi so outré that it would keep the media panting for an answer 20 months later.

The inquest continues this week. The mystery of how exactly Gareth Williams died, one fears, will go on much longer.

Remarkable coincidence?

Whatever the truth in the case of Gareth Williams, details of women's underwear and cross-dressing regularly emerge in the "presentation" of the deaths of intelligence agents.

Nicholas Anderson, former MI6 officer turned author, told The Independent on Sunday: "I am on verbal record to my own family, close friends and select lawyers that if anything ever happened to me – a straight man and a positive thinker – it would likely be made to look either like a suicide or that I died dressed like a woman.

"Over the years, it seems to me a favourite way of presentation. I, of course, am not suicidal in any remote way nor do I like to dress so. When I read in the press about Gareth Williams, women's clothes, and a wig, it all fits the usual scenario."

The IoS has come across at least 17 mysterious deaths – some dubbed suicides, others freak accidents – of MI6 agents, workers at GCHQ, or those linked to the defence or intelligence services over the past 50 years. Sexual overtones, asphyxia, or both, feature in a third of cases, and they are just the ones that are in the public domain and "open source", as spooks would say.

Stephen Drinkwater, 25, a clerk employed in a department at GCHQ where highly classified documents were copied, was found dead in his parents' house at Cheltenham in September 1983. A plastic bag was over his head and he had died from asphyxiation.

In March 1990, British journalist Jonathan Moyle, 28, who had been investigating claims that US civilian helicopters were to be converted into gunships for sale to Iraq, was found hanged inside a hotel wardrobe in Santiago, Chile. Eight years later, an inquest concluded that he had been "unlawfully killed" by a "person or persons unknown". Speaking in September 2010, his former fiancée said: "The British intelligence services tried to smear Jonathan suggesting he was sexually deviant."

Four years later, in February 1994, Conservative MP Stephen Milligan, 45, was found tied to a chair wearing women's underwear and with a bag over his head and a satsuma stuffed into his mouth. He was the parliamentary private secretary to the then defence minister Jonathan Aitken. Mr Aitken has since denied media reports that he also worked for MI6.

The same month that Mr Milligan's body was discovered, James Rusbridger, 65, ex-MI6 agent turned journalist, was found hanged at his house on Bodmin Moor in Cornwall. He was dressed in a green protective suit, green overalls, a black plastic mackintosh and thick rubber gloves. His face was covered by a gas mask and his body was surrounded by bondage pictures. Consultant pathologist Dr Yasai Sivathondan said he died from asphyxia due to hanging "in keeping with a form of sexual strangulation".

In another case, an inquest in July 1997 heard how GCHQ worker Nicholas Husband, 46, was found dead wearing women's clothing after a bizarre sex ritual. Mr Husband, from Tewkesbury, had a plastic bag over his face and was wearing a nightie and a bra. He was found dead after he failed to show up for work in December 1996.

In March 1999, Kevin Allen, a 31-year-old linguist at GCHQ, was found dead in bed by his father at his home in Cheltenham. He had a plastic bag over his head and a dust mask over his mouth. An post-mortem revealed that death was due to asphyxiation.