Specks of mystery DNA were discovered on the bag encasing the curled-up body of MI6 spy Gareth Williams, an inquest has been told.
Detective Chief Inspector Jackie Sebire said "two minor components of another contributor's DNA" were found on the zip toggle and padlock.
The evidence came to light as she appeared to rule out that Mr Williams got in the bag himself.
She said her officers had looked at "all aspects" of possibilities, as footage of the red holdall bulging with his body shape was played for the first time, the Press Association reported.
Ms Sebire told Westminster Coroner's Court: "My thought or my opinion since I went into the scene is that a third party had been involved in the death or by putting the body in the bag. So my primary focus was looking at the bathroom."
Video of the immaculately kept flat at the centre of his death riddle showed a cutting from the Observer newspaper headlined "top five regrets of the dying".
The video took the inquest on a walking tour of his Pimlico home, showing a woman's red wig, lipstick and make-up, in the condition that it was found.
Footage then showed close-up images of the white bathroom suite where Mr Williams's body was found.
The film zoomed in on the red North Face bag, showing bulges from his limbs inside and a brass padlock locking two zips together from the outside.
Mr Williams was found in the foetal position in the bag, there were no signs of struggle and his body position appeared "calm", Ms Sebire said.
Ms Sebire said she would have expected to find fingerprints left by Mr Williams on the bathroom tiles.
"Certainly there were no prints of anybody's in the lower-tiled wall," she added.
"He was in the foetal position. His legs were folded up towards his chest, his arms were bent slightly inwards."
She added: "In my opinion he was very calm. His face was very calm. His hands were resting on his chest."
Mr Williams had not damaged the bag or sustained injuries to his hands, the detective said.
"He was very muscular, he trained regularly. It is only my opinion but I would at least expect some tearing to the netting."
Ms Sebire, who described how the top-floor flat was hot and stuffy, said her inquiry had explored all possibilities over 21 months.
The officer, who received 200 items of information from the public, added: "It was a very extensive inquiry. We have looked at all aspects of it."
Ms Sebire said she allowed a counter-terrorism officer from SO15 - the only command at Scotland Yard with regular contact with MI6 - into the flat.
But she said she was solely responsible for investigations into the death.
The last computer evidence of him being alive was Mr Williams looking at a cycling time trial website on 16 August, the officer added.
Mr Williams's sister, Ceri Subbe, sat in the hearing without her parents as images showed the scene which greeted detectives as they arrived at his flat on 23 August 2010.
The flat gave an insight into the codebreaker's mind, showing carefully arranged piles of books and an extensive CD collection.
There was no sign of a break-in at the flat, with footage showing Mr Williams had left cash in a cupboard and a mobile phone on the living room table. There was little clutter and mess in the flat except for a dressing gown and quilt discarded on the bedroom floor.
Ms Sebire said: "I also found it difficult to explain because of his general tidiness. In my opinion, it was not something that was easily explainable."
Ms Sebire detailed the forensic evidence found there, including blood and semen.
The communal front door was secured by a mortise lock and union lock, and a spot of someone else's blood was found in the communal hallway, the inquest heard.
Inside the flat itself, an "old" and "very small" spot of Mr Williams's blood, which could have been from a cut, was found on the carpet near the stairs, Ms Sebire said.
She accepted that the blood could have dried over the course of a week.
Two shoeprints detected in his kitchen were too "partial" for the size or wearer to be identified, she went on.
In the larger of his two bathrooms, the only "significant finding" was traces of semen staining on the floor by the sink, which tested positive for Mr Williams, the detective said.
Traces of his semen were also found in the main bedroom, including on his quilt, she added.
Ms Sebire also described the "high-value" items found in the flat's smaller bedroom, which included 26 shoes and boots, mainly bearing designer labels such as Christian Louboutin, Stella McCartney, Christian Dior and Chloe; wigs wrapped in net packaging, which "appear to be unused", including one Mr Williams had bought on his recent trip to the US; small and medium-sized female clothing worth an estimated £20,000, all "immaculate" and "in pristine condition" and often in tissue paper; and make-up items including nail varnish and eye shadow that were "all new" and apparently unused.
The only used items appeared to be four pairs of the size 6 and 6.5 shoes, which was Mr Williams's size, Ms Sebire said.
Asked by Coroner Fiona Wilcox whether she thought the clothes would have fitted Mr Williams, the detective replied: "Possibly."
The clothes were found in a North Face holdall and on the bed, she said.
Receipts suggested they had been collected around 2008 and 2009.