MI6 codebreaker Gareth Williams was probably killed unlawfully but the case might never be solved, a coroner said today.
Fiona Wilcox said she was sure a third party locked Mr Williams inside the red holdall in which he was found dead.
She criticised the 21-month investigation as she said it was unlikely the riddle "will ever be satisfactorily explained".
"The cause of his death was unnatural and likely to have been criminally mediated," she said in her two-hour narrative verdict at Mr Williams's inquest.
"I am therefore satisfied that on the balance of probabilities that Gareth was killed unlawfully."
Mr Williams's family criticised his employers at MI6 afterwards for their response to his death, saying "our grief was exacerbated" by it.
His sister looked on as Dr Wilcox told a packed Westminster Coroner's Court that "on the balance of evidence" he was probably alive when he was put in the bag.
Dr Wilcox said it remained a "legitimate line of inquiry" that the secret services were involved in Mr Williams's death.
But she said "there was no evidence to support that he died at the hands of" spies as the inquest drew to a close.
She ruled that "it would appear that many agencies fell short" during the inquiries into his death.
Despite a 21-month police inquiry and seven days of evidence, "most of the fundamental questions in relation to how Gareth died remain unanswered", she said.
Mr Williams was suffocated by carbon dioxide, possibly as an onset of a short-acting poison, the coroner suggested.
She dismissed speculation that Mr Williams died as a result of some kind of "auto-erotic activity", also denying there was any evidence to suggest claustrophilia - the love of enclosed spaces - was of any interest to him.
"I find on the balance of probabilities that if he had got into the bag and locked himself in, he would have taken a knife in with him," she said. "He was a risk assessor."
MI6 apologised for failures in raising the alarm about his disappearance earlier as Dr Wilcox said several factors hampered inquiries.
Breakdowns in communication by her own coroner's office in ordering a second post-mortem examination, a DNA mix-up by forensics and the late submission of evidence by MI6 to police were singled out for blame.
Dr Wilcox also questioned why details of Mr Williams's private life were leaked to the press.
The coroner ruled out Mr Williams's interest in bondage and drag queens as having any bearing, before adding: "I wonder if this was an attempt by some third party to manipulate the evidence."
She found it "highly unlikely" that Mr Williams got inside his red North Face holdall alone, saying: "If Gareth had been carrying out some kind of peculiar experiment, he wouldn't care if he left any foot or fingerprints."
Referring to claims that he was interested in bondage, the coroner added: "I would have expected much more internet activity to have been recovered."
Mr Williams, a 31-year-old fitness enthusiast originally from Anglesey, North Wales, was found naked, curled up in the padlocked holdall in the bath of his flat in Pimlico, central London, on August 23, 2010.
Pathologists said he would have suffocated within three minutes if he was alive when he got inside the 32-inch by 19-inch bag.
Poisoning and asphyxiation were the "foremost contenders" in solving the death riddle, they said.
Bag experts said that even renowned escapologist Harry Houdini would have struggled to lock himself in the bag, while Mr Williams's family lawyer has suggested the "dark arts" of the secret services were behind the mystery.
Police recovered no evidence of a third party being present and have no suspects in their inquiry.
Dr Wilcox said in her verdict that the "highly unusual circumstances" of Mr Williams's death immediately raised the possibility of foul play, which had prompted "endless speculation".
"I find that this did affect the quality of the evidence that was heard before this court," she said.
But the coroner added that "taking all these shortfalls together, I am satisfied that the evidence is reliable and that we do not have to adjourn at this point".
The lack of hand and footprints in the bathroom was "significant", Dr Wilcox said, telling the court: "In relation to the prints found within the bathroom, in my view what was more significant was what was not found rather than what was found."
Revelations that MI6 failed to raise the alarm about his disappearance for more than a week prompted elaborate conspiracy theories about his job and private life.
Several years before his death, Mr Williams tied himself to his bed and had to be cut free by his landlord and landlady, the inquest heard.
It also emerged that the bachelor stored £20,000-worth of women's clothes in his immaculate flat and was fascinated by drag queens.
But Dr Wilcox said today there was no evidence to suggest the spy was a transvestite "or interested in any such thing".
The make-up found in his flat was more likely to reflect his interest in fashion, she argued.
And the wigs that were found there were "far more consistent with dress-up such as attendance at a manga conference", she added.
There was some suggestion that his interest in female footwear could have been of a sexual nature, but this was not unusual, Dr Wilcox observed.
"Gareth was naked in a bag when he was found, not cross-dressed, not in high-heeled shoes," she said.
Mr Williams would have been unlikely to invite a third party who was not a family member into his home, Dr Wilcox said, adding: "If a third party was present at the time of his death, in my view that third party would have to have been someone he knew or someone who was there without an invitation."
If someone else was there without having been invited, "that raises the possibility of an illegitimate purpose on the third party's part", she said.
"Gareth may have worked out a technique how to get into the bag and lock it from inside but I find it extremely unlikely that he did so."
Mr Williams was unhappy living in London at the time of his death and complained to family of "friction" at the intelligence agency.
He hated the post-work drinking culture and "flash car competitions" and was due to move back to the West Country a week after his naked body was discovered.
Secrecy surrounding his job proved a stumbling block as Scotland Yard murder detectives were not able to speak to his MI6 colleagues directly.
Scotland Yard has said it will review lines of inquiry, with fresh attention on the expert mathematician's colleagues.