Question: When Bourne interrogates Nikki (under duress) in the underground station, Nikki insists that Bourne had never worked in Berlin, much less completed his first mission there. But it is established that Bourne had killed the Neskis in Berlin on what is described by Conklin as his first mission. Assuming Nikki has no reason to lie and that she would have accurate information about Bourne's activities, what might explain that issue?
Chosen answer: Conklin ordered Bourne to kill the Neskis, telling him it was a training mission, when in fact it was an unofficial, off-the-books assignment to cover up his and Abbott's corrupt dealings with Gretkov, which Neski was about to expose. Nicky did not know about this Berlin mission as it was not an official Treadstone operation.
Conklin did not tell Bourne that it was a training mission. Conklin told Bourne "this is not a drill soldier...this is a live project, you're a go."
Partially correct. After Bourne eliminates the Neskis, Conklin says "Congratulations soldier, training is over." This implies that while the mission was real, Bourne was still an asset in training, and off the books.
By "not a drill" and "live project", Conklin is telling Bourne to actually kill the Neskis - like killing the hooded man for Hirsch, it's training him to do anything for Treadstone. It could be that the edit is out of chronological order, but the order of the scenes implies that after Bourne has done the job and returned to the car, Conklin says "Congratulations, soldier. Training is over."
Answer: Conklin was using Bourne for an off-book hit on the Neskis because Neski knew about the stolen money and the oil leases. Bourne was told it was a genuine "hit" for patriotic purposes, but it was not.