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Interesting fact: During my rewatch I've discovered the Turtles recovered 50 out of the 60 (I think it was 60?) mutagen canisters that sprinkled over NYC. How do I know this? Easy:
In the episode they change April's father from a mutant bat back to normal, Donatello says he needs 10 cans of Mutagen to make 1 vial of retro-mutagen. In the episode they had two vials of retro-mutagen, one that smashed on the floor by accident on the streets, and the one that changes April's father back to normal. This implies Donatello had to have 20 canisters of mutagen.
Later on when Karai is a mutant snake, Leo sprays one vial of retro-mutagen on her, but it doesn't have affect. This implies they collected 10 new mutagen canisters off-screen.
Later on at the Season 4 finale, once again Don has two vials of retro-mutagen on him. One they use to turn Baxter from a fly back to normal, and the other they use on Super Shredder but it doesn't work. This implies they had to have collected 20 more mutagen canisters.
Finally, the missing mutagen canisters were the backstory to the mutants: Kirby bat, the Squirrelnoids, Fungus Humugous, Pizzaface (if you count him as real and not a dream), Sir Malachi, and Mondo Gecko. In all these eps they show a flashback of the mutagen canisters raining from the sky, and they say these are how these mutants got mutated.
So if you add this all together, this basically accounts for around 55 out of the 60 missing mutagen canisters. That means they basically found nearly all of them besides the ones that cracked opened and created new mutants.
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