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To be fair, all of those powers are related to each other. She's immune to mutagen because of the Kraang/Utrom genetics. She has those powers because she's half Kraang/Utrom (because that's what they are at their cores, just trapped under the power of one individual) and has been learning to use those powers - granted, without anyone to train really train her and the Aeons inadvertently screwed up by giving her a crystal.
Imagine giving a newborn lamb of a novice digital artist the most high-tech graphic tablet there is with no instruction, telling them it would help her learn - and you're an professional architect with decades of experience. Also, that graphic tablet has the ghost of a long-dead architect that makes the digital arts student have Gollum levels of possessiveness over it.
It's all still very half baked, the phrase I always use regarding this telling of TMNT, and there's pretty much nothing that can be done to fix it at this point.
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