The coroner says it is "highly unlikely" Gareth got into the red bag alone in the bath - there should have been foot and fingerprints in the vicinity.
Coroner Dr Fiona Wilcox revealed the extent of the police investigation into the death of MI6 agent Gareth Williams, while delivering a narrative verdict.
Police interviewed more than 200 witnesses.
110 CCTV clips were collected.
300 house to house inquiries were conducted.
During the narrative verdict, Coroner Dr Fiona Wilcox says two keys to the padlock were found under Gareth's body, two others were locked in a cash box
She adds it is "highly significant" none of Gareth's fingerprints were found on the tiles or the shower screen near the bag.
Coroner Dr Fiona Wilcox says Gareth looked "peaceful" in the bag, which was undamaged and he seems not to have tried to get out.
The Coroner says "many agencies" fell short of the required standard in handling of this case - police, MI6, LGC forensics and the Coroner's office.
Coroner Dr Fiona Wilcox says there is no evidence Gareth Williams was killed by an MI6 colleague but it remains a legitimate line of inquiry.
Dr Fiona Wilcox notes she was receiving evidence from MI6 during the inquest, despite its claim to have handed over all relevant material already.
She adds the lack of signed statements from MI6 staff affected the quality of evidence heard at the inquest
During her narrative verdict, the Coroner says she's happy there was no tampering of evidence at the scene by MI6 or counter terror officers.
Coroner Dr Fiona Wilcox says despite a police inquiry, involving counter terrorism and an inquest, most questions about Gareth Williams' death remain unanswered.
She says: "It is my view that it's unlikely this death will ever be fully explained."
Coroner Dr Fiona Wilcox has begun to deliver a narrative verdict at the end of the inquest into the death of MI6 agent Gareth Williams. Dr Wilcox will outline facts and conclusions and comment on some of the evidence.