Can anyone explain to me why the mc dies depending on the choice i make in this scene? How is this decision connected to the way he dies a couple of scenes later? Was i somehow supposed to know what was going to happen, or do we have to go back and make the correct choices so we don't get a game over? If that's the case, it completely breaks the immersion and ruins the experience, basing my opinion on this "ending" this vn definitely doesn't deserve all the praise it gets. I thought everyone agreed that games that have "wrong choices" that lead to game overs suck, the choices are there only as an illusion.
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Basically this is a "joke" ending, or maybe more accurately non-cannon one. If you read the following scenes, you can understand how Hisao ends up dying. This is not a direct causality link, it's the sum of his first week at his new school.
If Hisao fails to connect to anyone in Yamaku, he basically doesn't bounce back from his stay in the hospital. A route about this would be pretty much meaningless since it would only be Hisao moping all day long without socializing and reading books in his room until the school year ends. There isn't a specific day in the first chapter where there are choices that are just "choose your arc". The choices in the intro are already significant for the route that hasn't actually started yet.
The choices are actually pretty well laid-out, though the only criticism is that they're set in a specific order, meaning you could have started a specific route without having the chance to start another one. This is why a lot of people assumed the Emi route was the standard one, since you can enter it by making only one decision, while the others may require more.
If you have your mind set on someone, and have already played through the first chapter, you should be able to start their route if you keep the personality of the character in mind.