Takeshi Kogahara’s “Nagisa” is one of the darkest films to come out of Japan so far this year — in both senses of the word. In this fractured fever dream, secrets lurk in places where daylight doesn’t penetrate: a household closet that serves as both a children’s den and a prison; an apparently haunted tunnel that acts as a portal into a young man’s troubled past.

That young man is Fuminao (Yuzu Aoki), a surly university student who has moved to Tokyo from a broken home in Nagasaki. He isn’t much fun to be around (just ask his ex-girlfriend, played by Kana Kita), though it’s initially hard to tell if his aloofness is a pose or the product of a deeper malaise.

When some coworkers from his part-time job drag Fuminao to an eerie tunnel that was the scene of a fatal bus crash several years earlier, it prompts a reckoning with all that he’s left behind. Memories come back in a flood of images and associations, and the figure who looms largest in them is his younger sister, Nagisa (Nanami Yamazaki), who seems to have passed on.