Yes, the game's storyline has very sad parts.
When you have to run away and become a fugitive, I was afraid
When you finish your rescue base, I was proud, and my base looks like a skull (started as cubone)
When you destroy the meteor and have to leave your partner, I cried (a bit) even on my second time through
When you return to your partner, I was overjoyed
I think it was the music and the words on the screen durring your little spirit flight that got me.
"your partner is sad..."
"you will miss your friend"
*sob* and this was durring school lunch so all my friends saw me upset over a game.
Its like when you become attached to a character in a game, book, or movie and they die.