8. Final Fantasy Tactics
Final Fantasy Tactics is one of the all-time greatest games of the series, and it's not even a numbered entry. Filled with solid character portraits, sprites, and cut scenes the music is top-notch in a series already noted for its high-quality music, and the writing is pretty good even with an English translation considered very sub-par in many ways.
The story is rife with political intrigue, warfare, backstabbing, betrayal, and death with no less than two separate sisters given the 'fridge' treatment. In the end the hero, Ramza, fights against a false god and sacrifices the lives of himself and his friends to kill the demon leader.
Though their fates are technically left ambiguous. The last survivor of the group writes a scathing report to publicize all the evildoing of the church and reveal the truth - and he is burned at the stake for it.
Cut a few centuries into the future and our burnt friend's descendant goes about researching and publishing the truth - the idea being the course of the game is him reading his executed ancestor's report. But quite frankly, that means that even if he succeeds in bringing down the church, they were the victors for centuries.