Nier

Nier is a JRPG with a fairly interesting storyline and mehhh gameplay mechanics.  I love crazy plots, and this one ended up being really good - but the effort in backtracking through quest areas, the lamesauce "shades" instead of cool textured bosses, countless load screens, the amount of sloowww dialog you had to suffer though made me almost put this down multiple times - and indeed put me asleep more times than it should.  The save system forces you to be at a mailbox to save, so if you do fall asleep - you have to wake yourself up enough to backtrack or finish what you were doing.  That said - and like Dune, it was worth trudging through to get to the meat of the story.

This will be chock full of spoilers, so play this if you don't want to ruin the twists.

You start by defending your daughter Yonah from a shade attack, but things go wrong as she invokes the help from a mysterious book.  Cut to 1300 years later (yes) - and you are in a town with your daughter who is sick with this shade-scum stuff and you befriend a floating book who becomes your magical fount called Grimoire Weiss.  Through a series of not-so-interesting missions that essentially boil down to "find the big shade and kill it", you meet your other party companions - Kaine (foul mouthed, scantily clad chick) and Emil (emotional 12 year old with Medusa powers).

When fighting off a giant shade that attacks the town, Kaine sacrifices herself to be turned to stone in order to block a shade behind a door and your daughter is kidnapped by The Shadowlord.  

 Cut to 5 years later (I assume you've been searching the whole time for clues as to where Yonah is), Emil finds some obscure letter on how he can unpetrify Kaine, but becomes a freakish skull boy in order to get the power to do so.  Back on your main quest, and in typical RPG fashion - you collect the keys to enter the Shadowlord's lair where you fight Devola and Popola - the town main quest givers and your previous helpers.  In the course of defeating them, they reveal what's truly been going on.  The shades you've been killing are the last vestiges of humanity that have been corrupted, and everyone "alive" is a vessel waiting for the reunion with these souls that have over time unfortunately developed a sense of self and purpose.  The shade that has infected Yonah is the actual Yonah, and the Shadowlord is you - trying to reclaim their bodies.

When you defeat the Shadowlord in combat, Yonah-shade stops you and runs to her father saying there is another girl inside that misses her father as well.  She sacrifices herself, you execute the Shadowlord and presumably live happily ever after.

In new game+ you are given additional cut-scenes to humanize the shadow creatures you must destroy.