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The bad ending being the good one and vice versa (spoilers, obviously)

Comment from Serge Ulankin
Okay, I just feel like I have to save this thought I got after playing FEZ, so I'll do this here. Mind, that this idea is not unique, I googled and some people over the internet had similar thoughts.

Since FEZ is very meta, Gomez clearly understands that he is a character in a video game. So when you complete the game without all 64 cubes, there will be the ‘bad’ ending, with the universe collapsing around you, but in the end Gomez will play music. So this basically means that even though you failed to reboot the universe, somehow Gomez ended up alive and happy with his drums. He finally broke out of being a controlled character in a game and did what he loved.

While the ‘good’ ending means that you successfully managed to reboot the universe and nothing really changed. Gomez is still trapped inside a videogame. Drums stays dusty and untouched. There's no escape.

That is probably why some people love the first ending more, because inside their souls they fell that it is better.

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