The hitman who killed the judges in The Pelican Brief has gotten himself close to Julia Roberts's character and is about to do her in when someone shoots him instead at the last second. Who killed the assassin? How'd they know who he was and when he would make his move?
It was done by CIA.
At the end of the movie, the FBI director Voyles has this conversation with Darby
From the script:
Who killed the man who masqueraded as Gavin Verheek?
You mean the assassin, Khamel. Off the record, the man who killed Khamel is a contract operative hired independently by the C.I.A.
As to how did they know - Voyles was of course very suspicious and refused to follow President's order to "back off" from the investigation. CIA was also interested in removing this famous terrorist and both organizations were informed that he most likely has arrived in Denver.