This is one of the last achievements in the storyline: to 100% the game in a single game, you need to do this after Match 3 and He Trusted You..
Bring a dark heart to Snake outside the dungeon and watch the cutscene that unfolds. That's it.
You can't get a dark heart until given the ability in the Inquisitor storyline. You also need to have unlocked up to "Dark Organs" in the tech tree.