Spoilers as it is a question about end game. In the end, we have two options, either to let Pagan Min survive or kill him. I killed him, so obviously I can't redo that now. Apparently, if I hadn't kill him, he would have left whole of Kyrat for the player.
Now, question is, if that happens, technically, player replace Pagan Min. So, all those soldiers we were fighting becomes our own army. So, we should actually change factions, and start fighting against the golden path.
Sadly, I have no way to find out if it happens. Or if the game just glosses over that "whole kyrat is yours, you are my rightful heir" line from Pagan Min.
Best Answer
The Golden Path is leading a revolution in Kyrat. When dealing with the leader of the old regime, you've got two choices. Choice one is killing him, and choice two is sending him off to exile.
In either situation, you've basically routed his army, and the Golden Path takes over the government (such as it is...). Whoever you chose to back during the plot becomes the leader of a "free Kyrat" either way.
Basically, Min is giving up his government and agreeing to leave the country, and not really granting you control of his army.