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You're definitely not stupid, I ran out of time to do proper playtesting (and I don't have a proper tutorial), and the first puzzle is unfortunately particularly obtuse. This game really needs, like, five tutorial levels before the opening puzzle but I straightforwardly ran out of time. So, the trick is that you can only hit the second box on the left if you're moving forward in time. Anything with static on it follows your local timestream, and anything without it follows the global timestream, and so you can't interact with stuff that's in the global timestream if you're going backwards in time, because cause comes before effect.  The problem is that I didn't communicate that you can hit that second box on the left, or that you can hit those boxes at all, or that you can push them onto buttons. Also you can hit the boxes with left click.

Also, the door out of the starting room closes -at a specific time in global time-, which is also information you need to know to solve the puzzle which doesn't really get communicated but should have been telegraphed more clearly.

Oh no it's not a skill issue this game's just really difficult. The dying repeatedly is basically just how the game works. It's a yaoi game with kaizo mario difficulty because I was in a weird place when I made it. I recommend editing your save to skip levels you're stuck on. I don't really have any tips besides "shoot from as far back as possible, hold down the mouse button instead of clicking, and memorize the timing pattern your gun fires/reloads in".

I won't be adding a crosshair or ammo counter because I initially had both of those things and removed them on purpose.

Your save file can be found in the "Bossfight she loved you_Data/Data/Saves" folder. There's instructions telling you how to edit your save file. The value you're editing is called "level" not "currentScene" which is what the instructions says it's called, because evidently I changed a variable name at some point and forgot to update the instructions. But the rest of the instructions are correct.