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In Rise of the Teenage Mutant Ninja Turtles, the Yōkai have a more specifically mutant origin than the yōkai of Japanese myth, having lived in a society that has evolved in a vast underground chamber now called the Hidden City. Because of this, the Yōkai comprise a people and culture that sets them apart from other mutants in the series who mostly only recently mutated because of the intervention of Baron Draxum, a Yōkai alchemist.
The Yōkai were originally mutated by a substance called Empyrean which spilt out of the Crying Titan, the most sacred place in the city. It wasn't until the series finale, "Rise", that the source of this Empyrean was explained: Within the Crying Titan lay the long-dead skeletal remains of a Krang with a stash of ooze.