SPOILERS AHEAD!
Fair enough. Even the 'bad' ending isn't really dark per say. When you're asked about submitting to benevolent will of the parents, if you no, things at first seem to progress as normal, but when MC interferes with the fight between Cato and Amicus and gets killed, he is left to become part of the Amalgamation and is not revived.
As for the second ending of the game, the one revolving around the three choices, if you pick at least two 'B' answers, when you get to the late game scene where the Monitor shows you what your future will be line (in route A), instead of getting that, you are faced with the spirit of Meera, and are actually TOLD of the plans that are made for you, unlike in route A where you are not told anything about it. You end up discovering though that the illusion of Meera was actually the Other.