There are three stages that we see when it comes to this shocking ending, so let's break it down:
Doyle shoots Mulderig.
Doyle runs after Charnier, and there's a shot.
Slides showing the fates of each real-life character, ending with the news that Doyle (apparently alive) and Rosso were transferred out of narcotics.
The original script didn't include #3, preferring instead to leave us in the dark. (That would have been even more maddening, in our humble opinion).
But this ending is still pretty frustrating. What do you think happened to get Doyle and Rosso kicked off narcotics? Was it because Doyle shot Mulderig? Was it because Charnier got away? Was it (okay, it's a stretch) a promotion?
We'll have to wait until someone makes The French Connection II: 2 French, 2 Connection to find out.