After he's framed for murder, a young man must go on the run from the CIA with a ruthless assassin in order to shut down the black market crime syndicate that killed his parents and stop a devastating terrorist attack.

Good point. The CIA does not get involved in routine homicides. He had to kill someone critical to national security -- outside the borders of the US. If the crime is committed in the US, he would be pursued by the FBI.

Why is he running from the CIA for a murder charge?

>> he?s implicated

If he was framed, then say "framed"

And I still don't see how the framing has anything to do with what follows. It may be a problem, may be a ruse, but there doesn't seem to be a direct cause and effect between the framing and having to help the assassin. The protagonist's motivation for helping the assassin is to find the killer of his parents when, given the inciting incident, it should be to clear his name.

If his goal is to find who killed his parents, then the logline should have an inciting incident that is clearly linked to that objective goal. A logline reader shouldn't be left wondering or guessing how the inciting incident is causally linked to the objective goal.