The few seconds at the end when Bourne takes the mook's gun, and ends up shooting it upside-down with his pinky, Guns Akimbo to nail the second one, then throws the dead body over the rail, jumps on top of it, and headshots the third goon while fucking free-falling, and hits the floor eight stories below, with the body as a pad, and then gets up. Admittedly, he's still very badly injured by the fall, but it's awesome nonetheless.
He nearly killed an knife-wielding assassin in an apartment with a pen. Awesome enough for CinemaSins to take a sin off of the film.
It's not just that. For the vast majority of the fight (save a few decent hits), Bourne beats the shit out of the assassin. This is probably someone who has a long and successful career as a Treadstone operative, and Jason Bourne took him apart like tinker toys.
During said battle, the assassin performs a Groin Attack on Bourne. It doesn't work.
Bourne reads a road-map of Paris for about a minute, and in that time, manages to memorize every road, alley and sidestreet like he lived there all his life. He notes the location of a car park, then outdrives the police in a beat up Mini Cooper.
Bourne managing to completely outmaneuver the Professor who is closing in on the house where he is hiding. He gradually outwits the much better armed agent, smoking him out of his camouflaged surroundings before taking him down with an antiquated shotgun.
Bourne reeling off to Marie all of the little clues he picked up while they were taking a break in a diner, to demonstrate just how ridiculous his skillset is. He memorized half a dozen license plates, performed a threat assessment on everyone in the building, identified all exits and potential weapons caches, and determined that he could run for a half-mile at a full sprint before oxygen becomes an issue based on the elevation. He did all of this while having coffee, and he did it all on pure muscle memory. The Treadstone training program must be insane to create agents able to do these things unconsciously.
