You cannot miss this achievement.
You will be rewarded with an achievement called "End game" worth 50G once you beat the game.
If you can't wait for your achievement, you can skip the credits after the final showdown. Or you can let the credits roll and enjoy some awesome 80's action movie soundtrack FarCry3: Blood Dragon has. Your choice!
You can get this achievement in any difficulty.
After you have finished the main story, you can return to the island and go after unfinished business as you might have experienced in FarCry3.