Jason Bourne: We don't have a choice.
Marie: Yes you do.
Pamela Landy: You wanna to go home? Find Jason Bourne.
Jarda: Word in the ether was you'd lost your memory.
Jason Bourne: You still should have moved.
Marie: Because sooner or later, you remember something good.
Jason Bourne: I do remember something good. All the time.
Kirill: You told me I had one month off.
Gretkov: You told me Jason Bourne was dead.
Nicky: They know you were there.
Jason Bourne: Stop, stop! A weeek ago, I was 4,000 miles away, in India, watching Marie die. They came for me, and they killed her instead. This ends now.
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.
Sierra1 ★
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."
Sierra1 ★