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Before the meeting could take place, Dr. Amarak is presumed killed when Olympic Carrier is destroyed by Lee "Apollo" Adama and Kara "Starbuck" Thrace after the Cylons appeared to commandeer the vessel and threaten to use a nuclear warhead placed aboard the liner to cripple the Fleet.
Later, a copy of Number Six, calling herself "Shelly Godfrey," arrives aboard Galactica, claiming to be an assistant of the late Dr. Amarak. She presents video evidence of Gaius Baltar's complicity in the Cylon attack. However, after analysis, the evidence appears to be fabricated. When attempting to follow up on this matter, Godfrey disappears and cannot be found throughout the Fleet (Six Degrees of Separation).
As Amarak is never seen or heard on-screen by viewers, it remains unclear whether or not Amarak was actually aboard the Olympic Carrier, a Cylon Agent, or whether the use of his name in these events was part of some other scheme by the Cylons.