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Tear Jerker: Princess Mononoke
The ending; between Joe Hisaishi's sublime score of "Ashitaka and San", the message that despite the fact that humans can be bastards and have serious flaws, there is always hope for them, and the last shot of a Kodama appearing in the ruined, yet rejuvenating forest, one line of dialogue is all it takes to kick it off:
"...I never knew the Forest God made the flowers grow."
The person right behind him. She was covered in bandages, and looks shocked at being all better. That person was one of the lepers that Lady Eboshi took care of. Leprosy was a death sentence back then, and that person was pretty much brought back from the dead.
Also, the film can be viewed as a Creation Myth for Industrialisation: It's the moment where humanity, not understanding the damage it's caused, started taking more than nature had to give. Until then the forest had been able to hold its own but it had been weakening the whole time. And the natural world no longer has its gods to protect it. As San says, "The forest god is dead", and it won't be the same anymore. The death of the forest god can be said to be the beginning of our climb into the present day world, and it's come at a terrible cost.
What makes the film so profound is that hatred and love is found on either side. Even the forest creatures have somewhat understandable but irrational hatred for the humans. Examples of hatred: the wolves initially want to kill the human protagonist, the lead boar is demonized out of his desire to battle instead of focusing on living, the villagers have hostility toward the animals, the humans go to war. Examples of kindness: the Forest spirits guide the humans to safety, the protagonist has a loyal non-human friend, etc.. And the protagonist manage to achieve a peace between all cultures and lives.
How about just 10 minutes into the movie, when Ashitaka is banished from his village ... and Kaya comes out against the rules to give him her crystal dagger so he won't forget her.
Any time that "Adagio of Life and Death" plays. It's such a heartbreakingly beautiful track, that contains both sadness and hope - the scene where Moro and Okkoto die due to the Forest Spirit and Ashitaka races to save San is particularly poignant.
The scene where the Kodama are all falling from the trees, fading out as they go. Peaceful creatures, having nothing to do with the wars around them, dropping like flies.
What about when Okkoto, limping away from the catastrophic loss against the Irontowners and Jigo's men, confuses the skin-wearing people for his warriors and tries to lead them back into combat? Only to be poisoned by them and become a senseless monster? His blind hope and desperation is terribly sad.
When San stabs Ashitaka for saving Eboshi's life, he barely flinches, and even hugs heras the beheaded Forest Spirit is tearing up the forest.
It's hard to watch the scene of Ashitaka cutting his topknot off, as the Emishi elders lament what will happen to their tribe now their last prince is leaving them forever.
This troper always feels close to tears during the scene where Ashitaka is too weak to eat himself, so San chews the food up first and then give it to him. Ashitaka is tearing up during that scene himself, it may be a factor...
San desperately clinging to the belief that she is a wolf whenever the differences between her and her brothers are emphasized.