The story began several years ago when Hamato Yoshi was betrayed by his disciple, Oruku Saki in his Martial Arts Clan. Escaped to New York, Hamato Yoshi was forced to stay in the sewer and befriended the rats.

One day, a young boy accidentially dropped his bowl of four pet turtles into the sewer. Hamato Yushi adopted them as pets.

Hamato Yoshi changed his name to Splinter. He renamed the turtles after his favourite artists, Leonardo, Donatello, Michealangelo and Raphael.

At the same time, Oruku Saki became the new leader in the clan and renamed it, The Foot Clan. To pursue his dreams of power, he renamed himself, Shredder and moved his headquarter to New York. Krang, a defeated alien lord was banished to Earth and he lost his body. To get back what he has lost, he ganged up with Shredder to obtain his goal. They made use of the newly created chemical, mutagen and transform two of the followers, Bebop and Rocksteady into two mutants after they failed their missions.

One day, Hatmato Yoshi returned to find his pet turtles covered with strange, shiny and murky liquid. Immediately, he cleaned them. Unknown to Yoshi, the liquid is mutagen, a chemical that transform any creature that contacts with it into a mixture form of whatever other animal he has contacted with. As a result, the turtles turned into human form while Yoshi changed into a human-form rat. They befriended with April O'Neil, a Channel news reporter.