Ben Zygier – aka Ben Alon, Ben Allen, Benjamin Burrows and "Prisoner X" – died in a secret Israeli prison cell in late 2010. Why was he there? Mr. Zygier, who'd emigrated to Israel from his native Australia about 10 years previously, had worked for the Mossad, Israel's external spy agency and something went wrong.

What went wrong? So far, his alleged crimes remain only a matter of conjecture. Israel asserts that Zygier was a threat to national security. How did he die? Israel says Zygier hanged himself with a bed sheet tied to a shower spout in his cell after almost nine months of mostly solitary confinement.

In a Dec. 2012 report released to the public today, an Israeli judge found that Zygier's death was a result of negligence by the Israeli Prison Service, since he was deemed a suicide risk.

Zygier's case, which the Israeli press was forbidden from reporting on for nearly two years, until the Australian Broadcasting Corp. broke the story of his detention and death early this month, prompts a litany of questions: About the practice of Mossad recruiting recent immigrants, and convincing them to spy on behalf of the country; about the extent to which basic legal protections can be overridden in Israel when the security authorities insist an individual is a threat to national security; and about what Zygier had done when he was in the Mossad's good graces, and what he did to fall out of favor.

The press has been full of theories about why Zygier was secretly jailed (not even his jailers were allowed to know his name), and why Israel continues to remain mum to its own public about his life and death. One theory that Prime Minister Benjamin Netanyahu's office sought to lay to rest today was that Zygier had reached out to Australian intelligence, perhaps in remorse at how Australian passports have been used to conduct espionage and assassinations by Mossad (the Israeli assassination team that killed Hamas leader Mahmoud Mabhouh in Dubai in 2010 used a number of foreign passports obtained from immigrants, including Australian ones). Mr. Netanyahu's office shot down that theory yesterday, writing that Zygier "had no connection to Australian security agencies."

But what was the reason Israel decided to disappear a young Jew who had emigrated to the country and agreed to join its clandestine service? These are, after all, the sorts of immigrants Israel is desperate to attract. No explanation has so far been provided. He was disappeared into his secret prison cell less than a month after the Mabhouh killing in Dubai, leading to speculation he was somehow involved. But anything solid so far? No.

Nor has there been a full accounting of the conditions of Zygier's detention. Most people who've experienced solitary confinement for long periods describe it as a form of torture that, when coupled with the fear and uncertainty of secret detention, are enough to push some people over the edge. The Israeli coroner's report says Zygier had traces of a sedative in his system at the time of his death, and a lawyer who met him a few days before said he seemed neither agitated nor depressed, given his circumstances.

Zygier's many aliases were made easier by Australian rules that allow one name change a year. Since the name "Zygier" might appear Jewish, he was encouraged to pick names like "Allen" and "Burrows" that did not, which allowed him to travel to countries like Iran and Syria under false pretenses to spy on behalf of Israel.

But in 2009, his frequent name-changing – and the fact that it was common knowledge that Israel's spy agencies recruit Jews in countries like Australia in order to take advantage of their passports – piqued the interest of Australia's intelligence service. In late 2009 Australian reporter Jason Koutsoukis, then working for Fairfax, received an anonymous tip that three Australians were using their identities to work for the Mossad, which had a front company selling equipment to Iran.

The source gave Mr. Koutsoukis Zygier's name and Koutsoukis spoke to him multiple times, including immediately after the assassination in Dubai. While Zygier denied the spying allegations, Australian intelligence officials confirmed to the reporter in early 2010 that three Australians who had become Israelis were being investigated for espionage. Koutsoukis published a story following after receiving that confirmation, and Zygier was whisked into secret detention soon after. Were Israel's spymasters angry and worried that he'd taken calls from a reporter at all? Or concerned that Zygier might be nabbed by Australia's security services, and so acted first? Possible.

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And that brings us to the most troubling aspect of Zygier's case, at least for many Israelis. Over the years, thousands of Palestinians have been held for extended periods of time without a trial or indictment on the sole basis of assertions from senior commanders that they are a threat to "security." While this, known as administrative detention, is quite common in the case of Palestinians, it is unusual for Israel to suspend due process for Israelis. Now, those sorts of methods appear to have trickled down to an Israeli citizen.

(This article was edited after first posting to correct the year of Zygier's death.)