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edit: Wait. If other animals mutated, where are all the other turtle people.
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Interesting question. Perhaps the exclusion of Turtle DNA was a deliberate snub to the TMNT?
I think if Stockman's and the Kraangs DNA banks shown earlier in the series were anything to go by then whoever made the bomb could have deliberately spliced a bunch of random animal DNA into the mutagen mix - a bit like shrapnel on a grenade - so not only is there the mutagen thrown out, but random DNA to splice it with.
It would explain the non native creatures, and horrific mixes of multiple creatures tend to cause nightmarish beasts like Justin or Mega Shredder, so those near the epicentre would have been likely to have been reduced to monsters that would have wreaked havoc.
I don't think the bomb would have destroyed humanity though - I think thats just Raph's perception of it. I think North America would have been screwed, and the damage to plants would have resulted in desertification - especially after 50 years.
I reckon the world just quarantined the area and abandoned it to the mutants running rampant there - which is why Oasis still survived because it was on the edge or just outside the quarantine zone.
As for it being the farmhouse, its possible, but I would have thought it more likely they'd have moved further than that, after all they were frantically running around in buggies and wartrukks - they would have covered a pretty major distance.