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Scratch (previously known as 'Pookey' before the mutation and as 'Hallocat' afterwards) was a truckers pet cat, his owner had been illegally dumping toxic waste for a chemical plant whose foreman did not want to dispose of the waste properly in an effort to cut costs. One day Scratch got under the foreman's feet, tripping him, and in a fit of anger the foreman picked Scratch up and threw him into a vat of toxic waste (which presumably was mutagen) and believed he had killed the cat. But Scratch mutated and along with two other mutant animals one an owl, the other a crow, seeked to get revenge on the chemical plant, and on humans in general.
The name Scratch is the name given to the characters action figure, which is also the rarest and most valuable TMNT figure ever made, as mentioned above, he was not called by that name originally.