MI6 officer Gareth Williams possibly died from poisoning or asphyxiation, a Home Office pathologist has said.
These were the "foremost contenders", Dr Benjamin Swift told the inquest into the death, but he added they were possibilities not probabilities.
Pathologist Dr Richard Shepherd said grazes on Mr Williams's arms could have been caused by attempts to get out of the bag in which his body was found.
Mr Williams, 31, from Anglesey, was found dead in his London flat in 2010.
The three pathologists who conducted post-mortem examinations, and who all gave evidence at Westminster Coroner's Court on Monday, had been unable to reach a firm conclusion on how Mr Williams died.
Dr Swift said he had found no trace of poison, which he said could have disappeared in Mr Williams's system during decomposition.
The pathologist found some grazes and bruising on the body, as well as three areas of internal bruising, but said these could have occurred accidentally - and that he did not think these suggested a struggle to get out of the holdall in which the body was found in an empty bath.
Dr Swift found no significant traumatic injury, no offensive or defensive injuries, no injury from sexual assault nor any bruising consistent with strangulation.
Dr Shepherd said he thought it more likely than not that Mr Williams was alive when he got into, or was put in, the sports bag.
He said it would have been difficult to put a newly-dead body into a bag in a bath "so neatly".
"There is nothing to suggest Gareth's body was manhandled into the bag," he added.
But he said he thought the grazing and bruises on Mr Williams's arms were "indicative of the type of injuries which could have been caused by rubbing his elbows on the inside of the bag to try to get out or to manoeuvre the zip".
"The balance of probability is that Gareth was alive when he got in the bag," he said.
"I think there could have been a period of awareness that he needed to get out. The length of time might have been short."
Dr Ian Calder told the inquest that if Mr Williams had entered the bag alive, the build-up of carbon dioxide inside would have become poisonous within two or three minutes, causing him to become confused and sleepy before eventually leading to loss of consciousness and cardiac arrest.
"He would get into a situation of not being aware, of not being able to react to getting himself out of the environment," Dr Calder said.
"I think it's a very likely possibility considering we have a healthy person with no damage, as far as we know no drugs, no trauma, no natural disease."
Forensic scientist Ros Hammond told the inquest there was "certainly evidence" of at least two unidentifed people at the flat in Pimlico, central London.
She told the court there were hopes of a breakthrough "within a matter of weeks" from DNA tests on a green towel discovered in the kitchen.
"The tests are still in progress and there may be some promising results from those tests," she said.
Dr Swift said he believed that Mr Williams died shortly after he was last seen alive on 15 August, because the level of decomposition was consistent with the length of time before his body was found on 23 August.
The pathologist said that it was the extent of the decomposition that had prevented the cause of death being ascertained.
He said the heat inside the bag, and in Mr Williams's flat where the radiators were on in the middle of summer, had increased decomposition.
The inquest was adjourned until Tuesday.
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