I think this minimal "motif" has been used in all Bourne-film opening sequences (and 1st track/Main Theme on OST albums) -- even Newton-Howard's score from Legacy.
In other series films, it comes a later and phrased a bit differently.
What I can't seem to easily identify is the exact instrument used to play this motif ... cor anglais, duduk, etc. Anyone with sheet-music access to these scores (or was present at the scoring sessions) outta know
Listen, then, for what might be called Jason's theme. First heard as the rogue espionage agent was found by fishermen floating in the Mediterranean in "The Bourne Identity" (2002), it only became an eerie, mournful bassoon solo because Powell couldn't make it heard over the sound effects of a storm otherwise.
"That was a happy accident. The opening for the first film used to have the tune written for bass guitar," says the 43-year-old British-born veteran of Hollywood. "I was trying to find something that would cut through the sound effects. What could I use that isn't too cliched? ... So in the end I used a high bassoon, not too cliched but efficient, poke through the sound effects. And I've kept it through all three movies."
Thx for that info ... I considered the bassoon as the woodwind source, but dismissed it as I though it'd would be too "comical" a choice for the mournful motif. I think Powell use of the "high bassoon" is effective.