This story is a sequel to Equestria Ninjas: Friendship School

The Rainbooms, the Turtles, and the Mighty Mutanimals go dimension hopping and land in a world populated by anthropomorphic animals living in an old Western setting. They decide to stick around and help a trio of law abiding cowboys protect their town from outlaws and other lawbreaking miscreants. Join the heroes who become the Ninja Cowboy/girls of Moo Mesa.

Contains no spoilers from Equestria Ninjas Friendship School

This story is a sequel to Equestria Ninja Girls

Picking up where they left off, the Rainbooms after escaping the planet earth's destruction at the hands of the Triceraton Empire are given a second chance to stop them from destroying their planet. They're transported from Equestria back to their world on board a space ship where the turtles and their friend the Fugitoid set out into space to stop the Triceratons and retrieve the Heart of Darkness.

Sequel to Equestria Ninja Girls. Highly recommend read first before reading this.

This story is a sequel to Equestria Ninja Girls in Space

After a mishap with a portal, the Turtles and their human allies find themselves joining the Rainbooms at Camp Everfree where there's mystery and magic in the air. With the Rainbooms gaining new magical abilities, they take their next step in their ninja training to learn to control their new powers and defend their friends from a danger lurking within the camp itself.

Sequel following the events of Equestria Ninja Girls in Space. Recommended to read before this.

Twilight and the girls of Canterlot High travel to New York to take on the Dazzlings who have allied with a mad man bent on revenge. The girls only hope to face the trio of sirens and their ally is in the form of four mutant turtles, their master, and their two human friends. MLP/Ninja Turtles crossover.

Inspired from a fan video.