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.

This story is a sequel to Turtles of Equestria

The Rainbooms and Turtles are back together again taking on old foes and new foes with the help of the girls of Crystal Prep and an old robot friend. But with a vengeful ex-principal out to prove the existence of their magic, they may be in for a load of trouble.

This story is a sequel to Equestria Ninja Girls: Forgotten Friendship

The Festival of Friendship is interrupted when the Storm King Invades Equestria. Now Princess Twilight and her friends and ninja friends must ban together and voyage to lands unknown to look for help to stop the evil King and save Equestria.

This story is a sequel to Equestria Ninjas: The Movie

After the Mutagen Bomb, the world was wiped out, leaving the turtles and the Rainbooms separated from each other. Now they must fight to survive in the apocalyptic wasteland from the threat of warring mutant gangs all while trying to find the only place left in the world that has any life to it.

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.

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.

This story is a sequel to Turtles of Everfree

After the death of Master Splinter, the Rainbooms and Turtles team up to take the fight to the Super Shredder with the aim of ending him once again for all to avenge their sensei. Will their combined strength and friendship be enough to overcome the rage and evil of the most powerful mutant they've ever tussled with?

This story is a sequel to Equestria Ninja Girls: The Shredder's End

After defeating Kavaxas, the turtles felt it was some time for a little break. So they join Sunset Shimmer in Equestria to meet some old familiar faces, and gain a little cultural experience. While also dealing with new threats and dangers as well. Still nothing has ever stopped these green ninja machines before, and they won't now.