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The "Neski files" are documents about the theft of $20 million from the CIA black budget seven years before the events of The Bourne Supremacy.
The files show that Yuri Gretkov stole the money with the help of Ward Abbott. Alexander Conklin also might have been involved, as the CIA discovers a large amount of money on his bank account after his death.
The theft involved Conklin (either unknowingly under Abbott's orders or because of his own involvement) to assign Jason Bourne for a first and unofficial mission to kill Vladimir Neski.
It is unknown if Neski collected the files himself or whether they are just named after his murder. Nevertheless, as an outspoken opponent of oil privatization, he was in Gretkov's way.
Years later, CIA Deputy Director Pamela Landy had the chance to buy the Neski files for $3 million from an unknown source. To undisclose the truth behind this, Yuri Gretkov ordered Kirill to kill the agents and the source, steal the documents, and frame Jason Bourne.