Not over yet. Boeing's deal with the DJ, which combined a small penalty (on top of already agreed payments) with white-washing of their criminal responsibility, is being challenged
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Families of the crash victims are suing the US. They accused the justice department of denying them an opportunity to weigh in on a criminal investigation into Boeing under a 2004 law meant to protect victims of crime and their representatives. They are asking a federal judge to force the department to turn over documents related to that investigation and to revoke the company’s protection from further criminal prosecution on the matter.
A recent Seattle Times article reports the "scapegoat statement" by an undisclosed FAA employee.