Origin: Spirits of the Past (2006) on Netflix

It is 300 years into the future. Earth's environment had been devastated by mankind's own foolish plans and humankind is beleaguered by the sentient forests which they have awoken. The world balance is tipped when a young boy named Agito stumbles across a machine that glowed in a strange blue hue inside a forbidden sanctuary. The machine, which has preserved a beautiful girl named Tula from the past, is activated. Tula has a "mission" that had been entrusted to her by the past ...