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Just watched the movie, but I could not understand the ending.

Spoilers ahead:

Conklin ordered the last assassin to kill Jason, right? Yet the assassin killed Conklin and Zorn (Conklin's subordinate) and said to Conklin's boss "It's done". Why?

Also, it was not impossible for them to find out that it was not Jason who got killed, but Conklin. From the scene, it appeared to me that they possibly knew everything.

What happened here? Can anyone explain?

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Being the Bourne fan that I am, I'd like to provide a more detailed answer.

Let's start from the beginning.

Bourne is pulled on to a fishing boat and doesn't remember who he really is. Meanwhile, the CIA receives word that the mission is a failure, which given the training, shouldn't happen. The CIA assume that Bourne has gone rogue, Abbot wants to bring him in, and Conklin has work overtime to do it.

Now, every assassin that Conklin sends, Bourne kills, which leaves a huge mess, something the CIA cannot be associated with, given that Treadstone is a highly top secret assassination program. In others words, it's becoming too public to fast.

Abbott realizes near the end, that Conklin cannot bring Bourne in, so Abbott has Danny Zorn contact the last assassin to take out Conklin. With Conklin out, they blame him, and move on.

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