A British intelligence agent was found dead, padlocked naked inside a gym bag, in the bathtub of his London apartment; there was no sign of a struggle, no witness, no fingerprints and no DNA evidence to explain how he died.

After three years of speculation about murder by foreign agents, targeting by the Russian mafia and an MI6 cover-up, Scotland Yard announced on Wednesday that they thought it was “probably” just an accident.

Their extraordinary conclusion directly contradicted the findings of Westminster Coroner’s Court which ruled last year that Gareth Williams, a 31-year-old code-breaker from Wales, was most likely killed unlawfully.

The police explanation that Williams had padlocked himself into the bag before dying alone in his apartment was met with widespread consternation. Martin Hewitt, the Deputy Assistant Commissioner at Scotland Yard, rejected suggestions that the police had been duped by intelligence services who wanted to ensure that the real reason for Williams’ death was never disclosed. “I do not believe that I have had the wool pulled over my eyes. I believe that what we are dealing with is a tragic unexplained death,” he said. “The Metropolitan Police’s position is that, on balance, it is a more probable conclusion that there was no other person present when Gareth died.”

He did admit, however, that they could not be sure what had happened in August 2010, when Williams went missing. “No evidence has been identified to establish the full circumstances of Gareth’s death beyond all reasonable doubt,” Hewitt said.

During last year’s coroners’ hearing, a lawyer acting on behalf of the Williams family said his death must have had a connection to his highly sensitive intelligence work. “There is a high probability that some third party was in the flat when Gareth was placed in the bag. Evidentially there seems to be no trace of an unknown party in the flat,” Anthony O‘Toole said in court. “Our impression is that the unknown third party was a member of some agency specializing in the dark arts or secret services.”

Williams was found in the curled up in the fetal position inside a red North Face bag in his bath. The bag had been padlocked shut but there was no evidence of anyone else being inside the flat. Police and family members said the trail may have gone cold because of the time that elapsed between the agent’s last sighting and the discovery of his body.

Officials at MI6, where he failed to show up for work, did not raise the alarm until August 23, a week later. A family statement released via the police on Wednesday said they were furious that the intelligence agency had not informed the police any sooner. “We still remain very disappointed over the failure of his employers at MI6 to take even the most basic inquiries concerning Gareth’s welfare when he failed to attend for work on August 16, 2010,” they said. “We believe that if proper steps had been taken in the same manner as any reasonable employer would have undertaken, further information relating to the cause of his death might have become apparent and not have been lost due to the length of time before Gareth’s body was found.”

Last year, Sir John Sawers, the head of MI6, apologized “unreservedly” for the agency’s “failure to act more swiftly.” The cause of that delay has never been fully explained.

After a secret meeting between the police and MI6 soon after the body was discovered, a team of counter-terrorism officers was asked to act as a buffer between the murder squad investigators and the security services.

Scotland Yard now admits that was wrong. “We didn’t get it right at the beginning and the way that we did it was cumbersome and didn’t allow us to do the investigation in the way that we wanted to,” Hewitt said, although he denied that any delay had allowed somebody to destroy evidence in Williams’ home.

“There is no evidence whatsoever to support the suggestion that Gareth’s flat had been subject to some form of ‘forensic clean’,” he said. “Indeed, finger marks and traces of DNA going back some years have been recovered, which tends to fundamentally disprove such a theory. Such a ‘selective’ clean would not be possible.”

Hewitt also appeared to downplay another of the theories that has surrounded Williams’ death. He said there was no clear evidence that the math prodigy’s interest in escapology or bondage, which he had searched for on the Internet, was linked to his death.

Last year’s inquest also heard evidence from his landlady that Williams was previously rescued from another awkward situation. Jennifer Elliot and her husband had let themselves in to Williams’ apartment when they heard cries for help at around 1:30am one night. They found him tied to his bed wearing nothing but boxer shorts. “He was embarrassed and panicky and apologized and said ‘I wanted to see if I could get myself free,’” she told the court.