Josephus's Antiquities of the Jews, written independently of the Mishnah and roughly a century closer to the events it describes, tells of a righteous man named Onias, renowned for having once successfully prayed for rain during a drought, who was caught up in the civil war between the sons of Alexander Jannaeus. One besieging faction demanded he curse the other side, then holding out inside Jerusalem. Onias prayed instead that God would judge fairly between both sides, refusing to take part, and was stoned to death by the besiegers for it.
Most historians identify Josephus's rainmaking Onias with the Mishnah's Honi, on the strength of the shared reputation and the closeness of the names, though the two accounts do not agree on how his story ends: Josephus has him killed during the siege, while the rabbinic tradition preserves separate legends about a later period of Honi's life, including a well known story of him falling into a seventy year sleep, without recording a death by stoning at all. The sources do not resolve the discrepancy, and the identification, though widely accepted, remains an inference rather than a certainty. Historically, the episode is read as evidence of a wider late Second Temple phenomenon: independent holy men whose personal, charismatic standing with God existed alongside, and sometimes in visible tension with, the formal legal authority the Sanhedrin was consolidating in the same period.