The series followed the continuity of the live-action films with the Turtles living in the same abandoned train station featured in the second and third films, Splinter's ear is slashed as it was in the original film series, and Michaelangelo's signature weapon being a pair of tonfa instead of his traditional Nunchucks which he gave away to Mitsu at the end of the third film. However the series contradicts the end of the second film where Shredder supposedly died after he drank the ooze that turned him into Super Shredder, but appeared pretty much alive and normal in this series.
The only Ninja Turtles related project to not feature April O'Neil or Casey Jones. There is a rumor that they were meant to appear in second season had the show not been canceled after one season, but it is unclear whether they would have remained in their villainous roles from when the project started off as a movie.
The Next Mutation project was originally a concept for fourth live-action movie. In this concept the Ooze that transformed the Turtles and Splinter was still in their bodies causing a much more drastic 2nd mutation. Michelangelo's mutation would have given him a more human appearance allowing him to walk among the people of the City. Donatello's mutation would have given him psychic abilities, but have him wear an optic device because his mutation would cause his vision to deteriorate. Raphael's rage would cause him to mutate into a fearsome creature with claws and spikes jutting from his body. Leonardo would have the ability to mutate his skin into different textures. Splinter would transform into a creature twice his size that he would have limited control over. The movie itself was designed around a fifth turtle named Kirby. However, the project got stuck in development and plans for a fourth theatrical movie was nixed. Though concept of having the Turtles mutate into creatures was later used in the 'New Mutation' saga of the Teenage Mutant Ninja Turtles (1987) cartoon. Soon after, Saban took over the Next Mutation project and made good on the promise of a fifth ninja turtle.
The designs the turtles have are heavily based on the movie IV concept art. However, since this moved into a TV project, it was decided that the turtles would also wear initialed belt buckles and colored elbow and knee pads since TV audiences were so used to the turtles wearing them in the Teenage Mutant Ninja Turtles (1987) cartoon show.
Saban Entertainment came in with Fox Kids Network and Fox Broadcasting Company after plans to make the Next Mutation movie fell through. When Saban and Fox asked co-creators Kevin Eastman and Peter Laird how they could make this project different, they mentioned the idea for a fifth turtle. Saban liked it but, insisted that the fifth turtle had to be female or they wouldn't green light the show. Laird, never a big fan of the male fifth turtle idea, very reluctantly agreed to add a fifth turtle since the original cartoon was ending and without a TV project Mirage Studios would need to downsize.