Here are a few of the things that pushed me away from the Mormon church during High School.
I was in Academic Decathlon, and one of the subjects that year was "The Brain". I read a number of articles about the brain, and it seemed to me that there was a very strong connection between the physical activity of the brain, and our subjective experience. This seemed at odds with the idea of a "spirit" in the Mormon faith. Specifically, it didn't seem like the spirit had any purpose. Everything we did and experienced seemed fully explainable by the brain. In addition to that, it seemed like in order for us to "live on" after we died, our spirits would need to essentially replicate everything that happened in our brain (since our brain would be decaying somewhere), and this seemed redundant.
I remember reading one article that gave me some hope. This article talked about microtubules in the brain, claiming that they acted as small quantum computers in some way -- and it seemed to me like there might be some tenuous connection between the Mormon "spirit" and quantum mechanics, since quantum mechanics was sufficiently mysterious to act as a scape goat. However, it seemed like this was the only guy claiming any such quantum effects in the brain, and as I learned more about quantum mechanics, it seemed like less and less of a mysterious scape goat.
My two best friends in Junior High and High School were not Mormon, and I never felt right trying to tell them that they should become Mormon. They seemed very happy: they had a good family, and good parents. I didn't feel like Mormonism had anything to offer them in terms of happiness. I suppose I should have thought "wouldn't they benefit from knowing 'the truth'?", but I didn't think that. Or rather, it seemed to me a bit weird to claim that I knew the truth and they didn't, since why should my belief be better than theirs just because I believed it? I'm sure I was also just self-conscious of being a salesman for the church. Anyway, it bothered me that the Mormon church would place my friends in a less-than-ideal eternal afterlife.
Feeling the Spirit vs Understanding Something
I really wanted to know whether God existed. I had been thinking a lot about the upcoming prospect of going on a mission, which would involve preaching the gospel for a couple of years. I believed strongly in the faith myself, but before I committed to convincing other people about it, I wanted to be more certain.
One day at school, I prayed about this issue. It was during seminary, which is like Sunday school during the week. I prayed very hard.. very very hard, and very fervently. And I got an answer. I was overcome with the spirit. I cried, and I was certain I had gotten my answer from God.
Of course, about 10 minutes later as I was walking out of the seminary building, I began to doubt my experience. I thought, how can I know that the feeling came from God? Maybe I just wanted to feel something so badly that my brain kindof snapped. I wasn't sure.
Later that day, I was in physics class. We were learning about sound, and about the resonance of organ pipes, and how this related to the speed of sound in air, and a sin curve. It made sense. Things clicked in my mind and I understood.
This feeling of understanding was also very powerful and very positive, and it did not carry with it an ominous sense of doubt -- not that I was sure my understanding was correct, but rather it made sense. It was somehow more tangible and lasting than the feeling of the spirt I had experienced before.
In any case, I decided in this moment that what I needed in order to remain Mormon was a similar understanding of the Mormon faith. That is, I needed it to make sense. Unfortunately, approaching the religion from this angle was the biggest death nail in my faith. It never made sense to me.