In an alternate, apocalyptic future that takes place fifty years later, all humans and most of the mutant population have been wiped out, due to an extremely powerful mutant explosion that had mysteriously occurred through unknown means. Only a weathered Raphael, who has most of his childhood memories lost to him, and Donatello (whose consciousness has been transferred into Metalhead) have been traveling throughout the Impossible Wasteland trying to save alive while being pursued by the Verminator and his bikers. Befriending a female meerkat warrior named Mira, the last of her tribe, who harbors the secret to "Paradise" and that she must find a wise turtle called "the Holy Chalupa."