Depositions against the gang began on 2 August 1866 and attracted great excitement. It was only now that it was revealed that Sullivan had informed on the others. On 7 August Burgess wrote a long statement - 'The Confessions of Burgess the Murderer' - in which he detailed many crimes and tried to exonerate Kelly and Levy.
The case went to the Supreme Court. A special sitting opened in Nelson on 12 September. Mr Justice Johnston of Wellington was appointed as trial judge.
In accordance with the amnesty, Sullivan was not charged. Burgess conducted his own defence. He was determined to implicate Sullivan directly in the killings and cross-examined him for 15 hours without success. When Burgess asked him why he had killed James Battle, the judge advised Sullivan that he did not have to answer.
On 18 September Johnston spent over six hours summing up the case for the jury. He described Burgess as an 'arch plotter' , a 'cruel assassin' and 'one of the wickedest of men'.
The jury took just under an hour to find the three guilty of murder. Kelly collapsed and was taken away sobbing, but Levy maintained his innocence. To secure convictions for the killing of Mathieu's party the government had decided that the safest and most efficient option had been to accept the testimony of Sullivan.
The government amnesty applied only to the murder of Mathieu and his associates. A separate trial for the murder of James Battle was held on 19 September and the jury took only 25 minutes to find Joseph Sullivan guilty. He was sentenced to death.
Regardless of how helpful Sullivan had been to the police, the public believed he was a murderer and had got what he deserved. Sullivan claimed he had a deal with the government, and the police supported his calls for a pardon. Police informants were an integral part of crime solving and future investigations might suffer if there were doubts as to the sincerity of any deals offered for information. The Superintendent of Nelson Province, Alfred Saunders, agreed. Consequently, Sullivan's sentence was commuted to life imprisonment. He was formally pardoned in 1874.