 If you liked
Sakasama no Patema
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 ...then you might like
Made in Abyss Movie 3: Fukaki Tamashii no Reimei
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Both are sci fi dark fantasy movies where the young protagonists venture and investigate a mystery of a place far and unfamiliar to them that they had unintentionally encounter and also features fitting and immersive music as well as many emotional moments and many mysteries that will live you wondering.
Both also features a antagonistic organization who is looking to captivate or exploit a young captive girl in their own ways and motivation.