On 5 October 1928 the body of Bayly's 17-year-old cousin Elsie Walker was found in bushes near a quarry at Panmure. She had a small bruise on her head, but it was initially unclear whether this was the cause of death. Elsie had been living with the Baylys at Papamoa for the past year and had gone missing on the night of 1 October. There were local rumours that Bill Bayly was involved in her death.

Public disquiet grew as an implausible scenario was constructed by the police: Elsie, a young woman who probably could not drive, was said to have stolen a car and negotiated 150 miles of back-country roads at night before abandoning the vehicle and walking eight miles to the quarry, whereupon she died, either from exposure or exhaustion. In December doctors decided that Elsie Walker had probably died of 'concussion following a blow on the head'. There was semen on her underclothing, but 'no sign of rape'.

The coroner's inquest, held in January 1929, found that there was no evidence to say whether the death had been accidental or homicidal. Bill Bayly and other members of his family all testified that he was in Auckland when Elsie Walker disappeared. The coroner, F. K. Hunt, criticised police bungling in the early stages of the investigation. Believing this meant 'suspicion may rest against a perfectly innocent man for the rest of his life', he called for a public inquiry.

The commission of inquiry, conducted by Edward Page, a stipendiary magistrate, reported in March 1929 that police enquiries had been 'prompt, thorough and exhaustive', and that existing procedures were satisfactory. However, in August New Zealand Truth revealed that two women were claiming to have seen Bill Bayly at Papamoa on the day of Walker's disappearance; there were suggestions one of the women had been attempting to blackmail his mother. Demands from women's groups for a reopening of the inquest were supported by the coroner. But on the same day that a petition of over 15,000 signatures was recommended for favourable consideration by the parliamentary public petitions committee, Minister of Justice Thomas Wilford declared that because the women's conflicting statements would not stand up in court, he would not amend the Coroners Act 1908 to enable a second inquest. Although the act was amended the following year, the case was never reopened.

Meanwhile, Bill and Phyllis Bayly had been dairy farming at Ruawaro, near Huntly, since November 1928. Their immediate neighbours were Samuel and Christobel Lakey, who had bought their property from Frank Bayly. Samuel had earlier worked as a carpenter for Frank at Ruawaro and at Karaka and Papamoa. Relations between Bill Bayly and the Lakeys were initially friendly, but deteriorated to the point where Christobel Lakey is said to have accused Bayly of having murdered Elsie Walker, saying also that she and her husband expected the same fate.

On 16 October 1933 Christobel's body was discovered lying face down in a pond near the Lakeys' farmhouse. Some speculated that her husband had killed her and perhaps himself, but it soon became evident that both Lakeys had been the victims of foul play. On 18 October bloodstains were found on a wheeled frame near the boundary between the Lakey and Bayly farms, and the following day the police began searching the Baylys' property. Bloodstains were discovered on Bill's sledge, guns missing from the Lakeys' house were found buried in his swamp, and chemical tests revealed charred bone fragments on a shovel taken from his cowshed.

In December Bayly, who had been under surveillance by the police, disappeared, leaving a suicide note. He soon surfaced in Auckland, and was arrested for the murder of Christobel Lakey. As the search continued, human bones and items of clothing were found in Bayly's garden. It appeared that Lakey, his best suit and a pair of boots belonging to a friend had been incinerated. On 10 January 1934 Bayly was charged with Samuel Lakey's murder.

The trial, before Justice A. L. Herdman, opened in Auckland on 21 May 1934. The prosecution, led by Vincent Meredith, took more than three weeks to present its case. 'Pathology, physics, ballistics, and photography contributed evidence…the probative force of which was convincing almost to a startling degree.' The defence called no evidence. Senior counsel Erima Northcroft spent nearly four days attacking the Crown's case, but on the 29th day of the trial the jury took barely an hour to find Bayly guilty on both counts. Petitions seeking commutation of the death sentence or a new trial were unsuccessful. Protesting his innocence to the last, Bayly was hanged in Mount Eden prison, Auckland, on 20 July 1934. He was survived by his wife and two young sons. The Bayly case aroused unprecedented interest at the time and has continued to fascinate the New Zealand public.