Naruto: Me, the Shikotsumyaku Byakugan Princess

From the start, a lone Kaguya girl dies at the hands of the Hidden Mist's Anbu amid a blood mist, then rises from a mountain of corpses and sea of blood.

Her mutated gray Byakugan and all-purpose Shikotsumyaku combine to give her a bizarre ability to control her own body, setting her on the path of a nonhuman taijutsu ninja.

Shikotsumyaku strengthens her bones, the Byakugan controls chakra and her body, Lightning Release Chakra Mode tempers her flesh, the reverse Eight Gates replenish her life force, devouring Tailed Beasts gives her an inexhaustible power source and a Tailed Beast Cloak, and the Monkey King grants her indestructibility...

A beautiful girl as delicate as a doll becomes a nonhuman taijutsu monster. The extreme gap between her overwhelming stats and mechanics, and between her appearance and combat style, creates a brutal Hokage story drenched in blood and gore.

(No transformations, single heroine, somewhat dark, nearly invincible, no System, no babysitting.)