The Bureau of Internal Investigation is a Federation organization created shortly after the Federation lost several major battles to the Aurorans. Federation leaders blamed the defeats on a Auroran spy network supposedly scattered throughout Federation worlds, and in response, the Bureau came into being.
Today the Bureau is the de facto head of the Federation, though ordinary civilians are unaware of this. They use enslaved Vell-os telepaths to manipulate the courts in their favor, and they routinely blackmail and torture those opposed to them.
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The Bureau, as the driving force behind Federation politics, is important in all six major mission strings, although it is less so in the Auroran string.
At the end of the Federation string, the player becomes the Head of the Bureau of Internal Investigation.
After one finishes the Vell-os or Polaris mission string, one occasionally runs across Bureau cells on Federation worlds. You can choose to go after them, but be prepared to fight around a dozen RAGE Gunboats.