On 31 October 1828, Burke’s lodgers, Ann & James Gray, became suspicious at Docherty’s disappearance, especially when Burke warned them away from the bed where her body was hidden. Waiting for him to go out, they quickly discovered the body, confronting Helen McDougal. Realising what they had seen, she tried to bribe them into silence, recruiting Margaret Hare’s help as well, but the Grays refused payment and made off to summon the police.
Helen and Margaret contacted their husbands immediately, who took Docherty’s body to Surgeon’s Square in a large trunk to secure payment. When the police arrived at Burke’s home, there was no body. An anonymous tip-off led police to the offices of Dr. Knox at 10 Surgeon’s Square on 2 November, where the body of Mary Docherty was found in a tea chest. William Burke, William Hare, Margaret Hare, and Helen McDougal were all arrested for her murder.
They all produced conflicting stories under interrogation. When news of the arrests became common knowledge, prostitute Janet Brown came forward with the story of the disappearance of Mary Paterson. Neighbours provided additional stories about suspicious activities, and a further search of Hare’s lodging house revealed clothing that had belonged to Paterson, as well as items identified as belonging to Jamie Wilson and Mary Docherty.
An autopsy of Mary Docherty concluded that she had died of suffocation, but could not prove whether this was intentional or accidental. The lack of direct evidence, linking Burke and Hare to the deaths, led the Lord Advocate to offer Hare the chance of immunity from prosecution, if he agreed to give evidence against Burke. Hare accepted with alacrity, and implicated Burke in all of the cases known to the police at that time. On 1 December 1828, Burke and McDougal were charged with the murder of Mary Docherty, and Burke was also charged with the murders of Mary Paterson and Jamie Wilson. Hare and his wife escaped all charges, although they continued to be held in Calton Prison until well after the trial.