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: They frame Bourne because Borne was actually the one who killed Neski and his wife (he was doing it on Conklin's orders). Once Pam Landy does some digging, she will realize this; then it's a simple matter of putting two and two together - the man who killed Neski would obviously have a huge motive for covering up his crime. This is why Abbot and Gretski frame Bourne: he's the perfect fall guy.