Freedom Hosting was one of the largest .onion website hosts until it suddenly started serving malicious code, and eventually went offline (presumably permanently).
What was the sequence of events that led to Freedom Hosting going totally offline?
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According to the Wired article FBI Admits It Controlled Tor Servers Behind Mass Malware Attack, "the FBI yesterday acknowledged that it secretly took control of Freedom Hosting last July". The article notes that "[i]t’s not clear how the FBI took over the servers". However, the comment that "the bureau was temporarily thwarted when Marques somehow regained access and changed the passwords" is suggestive. Perhaps the FBI obtained Marques' account credentials. Or perhaps it used social engineering or coercion. Additional details may come out in court.