It Was Different With You...
Bourne: Why are you helping me?
Nikki: It was different with you. Don't you remember?
Bourne: No.
Nikki: You snatched me out of a crowded area, brought me into a subway tunnel and repeatedly threatened to kill me. Then you pulled me into a secluded room and dry clicked a pistol against my skull while I begged for my life. Then I see you again not more than a few days later standing there gun pointed at me and what the hell was I supposed to think, that you were there to deliver flowers?
Bourne: Oh, right. Sorry about that.
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Joking aside, I loved the movie, but the romance angle is an arrow in the heel of an otherwise perfect trilogy. I don't care what Greengrass said in the commentary, the supposed romance between Nikki and Bourne was shoehorned in and all can ask is why?
It's hard to work out the timeline between Supremacy and Ultimatum, but lets assume that Bourne telling whatshisface that Marie is dead occurred well before he ran into Nikki again. I could be wrong, but that scene could have also taken place after he told Abbott, "She wouldn't want to. That's why you're still alive."
So now we have Bourne on a path of redemption, spurred by the memory of the woman he loves. He encounters Nikki shortly after the events in the hotel and suddenly he remembers how he threatened her but only after Nikki lied to the CIA to help him.
Maybe instead of this, "It was different with you," crap, she could just come right out and say, "Part of me was afraid of what you would do if I didn't help. But at the same time I felt awful about what we took from you and how I was a part of that."
Instead of a shoehorned romance, you have Bourne apologizing to Nikki and wishing he could take back those events.
I just think there could have been a lot more weight to the scene. Nikki's romance was so minute that you could have replaced it with anything and either you wouldn't have lost anything integral to the plot, or you could have had something ten times more meaningful to the plot and made it an even better movie than before.
Feel free to disagree, of course.
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