I watched a lot of IFC and Sundance films when I was in highschool (around 2006/07ish). I vaguely remember watching this indie Japanese film, but it's ending has stuck with me. A quiet guy is our main protagonist. There are 2 sisters (I believe) that he encounters throughout the film. About halfway through one sister dies, and the protagonist and the other sister retreat to her somewhat abandoned house. The two start growing closer and begin to become attracted to each other. At one point she falls asleep on his lap and he has a wet dream, and has to wash his pants.
The part that I remember the most is the ending, in which a group of men break into the house attempting to kill one or both of them. The protagonist kills all of them, and removes his shirt... where we see that his back is covered in tattoos revealing that he was Yakuza.
I'm probably on a government watch list for all of the crazy google searches I've made recently trying to find this title. Please, help me.