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So, in new thinking...
What if the turtle's mutations were deliberate?
Looking back at my idea for the Utroms being in a big turf war with the Triceratons, and what the Ooze was meant to be, I had the idea of it being like liquid Nanogenes from Doctor Who. It would only be meant to heal a specific DNA pattern, so when the healing agents don't recognize a pattern, they just make sh*t up and try to call it a day.
When it happens on accident with something, the Specimen 0 (might have to make that its own mutant, it sounds really cool.), the Utroms realize that such a thing might make a good soldier against the Triceratons.
Hamato Yoshi, one of their guardians, volunteers to mutate himself so the mutated soldiers in training can be more comfortable with something more like them. Afterwards, Leatherhead and the four turtles were mutated. However, Leatherhead imprinted on the Utroms a little too hard, so it came down to just the turtles. Yoshi trains them in the TCRI basement for seclusion, while not telling them of their origins for years "because they weren't ready".
Though, the Super Soldier program ends up falling apart somehow, but they decide not to give up on the four turtles and Leatherhead, who ended up learning combat in a different sense than was intended.
Before Splinter is able to tell the turtles of their origins, the MOUSERS come into the basement, with Baxter Stockman not knowing about the Secret Rat Man living below the TCRI building. Thus the turtles are forced to the outside world prematurely to look for their master, while the Utroms have to save Yoshi.
How Shredder and the Foot Clan fits into all this...I have no idea yet XD .
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