Thomas and Twilight Sparkle's Adventures of Teenage Mutant Ninja Turtles: Out of the Shadows is an upcoming Thomas/MLP/TMNT crossover to be made by Hiatt Grey. And the sequel to Thomas and Twilight Sparkle's Adventures of Teenage Mutant Ninja Turtles.


One year after their battle with the Shredder and Eric Sacks being sent to prison, the Teenage Mutant Ninja Turtles still live in secret, having allowed Vern Fenwick to take the credit for Shredder and Sacks's defeat. As Shredder is transferred between prisons with two criminals that were being transported alongside him, Bebop and Rocksteady, by corrections officer Casey Jones, his Foot Clan–operating under the direction of scientist Baxter Stockman–attack the convoy transporting him. The Turtles, tipped off to the attack by April O'Neil, intervene. Stockman is still able to affect Shredder's escape using a teleportation device, but Shredder is hijacked mid-teleport and winds up in another dimension. There, the alien warlord Krang gives him a mutagenic compound in exchange for his promise to find three components of a machine Krang sent to Earth in ages past, which will open a portal to his dimension when united, and he knows that Shredder and Stockman have the first piece. When Casey failed to transport prisoners, he decides to go on his own.

Shredder recruits Bebop and Rocksteady, who also escaped, and has Stockman use Krang's mutagen on them to transform them into powerful animal mutants - a warthog and rhinoceros, respectively. April witnesses their transformation, and is able to steal the vial of mutagen. Pursued by the Foot, she is rescued by Casey, using hockey gear. In the scuffle, the vial is taken into police custody. Donatello deduces that the mutagen could be used to turn the Turtles into humans, enabling them to live normal lives above ground, but Leonardo refuses and insists on keeping it a secret from the others. Michelangelo overhears their conversation and tells Raphael, leading to a fierce argument between the brothers. Furious, Raphael recruits Michelangelo, April, Casey, and Vern to break into the NYPD police headquarters and recover the mutagen. In the National Museum, Shredder goes with Bebop and Rocksteady to steal the second piece, before Leonardo and Donatello were also there. Vern distracts the police, while April and Casey come to retrieve the mutagen, but The Foot arrive ahead of them and in the ensuing battle, the Turtles' existence is revealed to the police, who react with fear and hatred. April and Casey intervene and let the brothers escaped, but April and Casey are arrested, and also see TCRI`s cameras, that April stole the mutagen. 

With Shredder's forces having already recovered two of the pieces of the portal device, the Turtles track Bebop and Rocksteady as they recover the final piece from the Brazilian rainforest. The Turtles intercept their jet on its return journey via skydive, and although the battle crashes the jet, Bebop and Rocksteady manage to escape with the final component. The Turtles return to New York and they do not want to be a team to this failure, as Stockman and Shredder complete the portal device and open the gateway to Krang's dimension, through which his modular war machine, the Technodrome, begins to emerge. Shredder betrays Stockman and has his men take him away to their headquarters in Tokyo, but upon entering the Technodrome, Krang betrays Shredder, freezing him and locking him away with his collection of other defeated foes. April calls Vern to find out about the camera that incriminated in TCRI.

Seeing no way to combat the Technodrome discreetly, the Turtles debate over taking the mutagen and becoming humans in order to fight openly, when Splinter tells them when making their decision. Though Leonardo agrees to do it, Raphael shatters the vial, realizing that they must accept themselves. Vern recovers security footage that proves Stockman and Shredder's crimes and secures April and Casey's release, allowing them to set up a meeting between the Turtles and police chief Rebecca Vincent, where they convince her that they aren't enemies and Vern also tells the truth to the police about capturing Shredder alone, as he enlisted the help of turtles first. The Turtles then go into action, are transported by police, and confront Krang aboard the still-assembling Technodrome. Meanwhile, Casey keeps Bebop and Rocksteady busy and defeats them by capturing them inside a container with a grenade, Rainbow Dash sends Diesel 10 into a barge of sludge, and the Mane 6 use the Elements of Harmony on Discord (since he is no longer immune to the elements), and then Princess Celestia appears and sends Queen Chrysalis far away, and Sweetie Belle shoots Diamond Tiara and Silver Spoon, Hiatt Grey's engines send Alter down the road, and Den and Dart flea, while April and Vern defeat Shredder's lieutenant Karai and take control of the portal device. The Turtles locate the beacon around which the Technodrome is assembling and hurl it back through the portal, taking Krang and the rest of the Technodrome with it. April, Casey, and Vern then shut the portal down. As he disappears, Krang swears he will return for revenge.

In the aftermath, Bebop and Rocksteady are taken back into custody, while Stockman remains at large. Karai and the Foot Clan are apprehended, being reported by April and with Vern, who return to Channel 6. At night, the Turtles are honored by Vincent and the NYPD, along with April, Casey, and Vern, and she said to give an opportunity to the people and accept them, but the turtles elect to keep their existence a secret from the public, but they will always have help when they want.