Thomas, Twilight, and Logan is the tenth upcoming Thomas/MLP/X-Men crossover made by Hiatt Grey. And is a sequel to Thomas and Twilight Sparkle's Adventures of X-Men: Apocalypse.
In the year 2029, mutants are on the brink of extinction, with no new mutants having been born in 25 years. James "Logan" Howlett, formerly known as Wolverine, spends his days working as a chauffeur in Texas. His healing factor has been severely weakened due to his advanced age and as a result the adamantium on his bones has started to poison him. Logan lives with mutant tracker Caliban in an abandoned smelting plant across the Mexican border, where they care for Professor Charles Xavier, who is suffering from a neurodegenerative disease which causes him to lose control of his telepathic abilities to devastating effect. One day, Logan is approached by Gabriela Lopez, a nurse for biotechnology corporation Alkali-Transigen, who wants him to escort her and an 11-year-old girl named Laura to a place in North Dakota called "Eden".
After reluctantly accepting the job from Gabriela, Logan discovers that she has been murdered. He, Xavier, and Laura narrowly escape from her killer, Transigen's cybernetically-enhanced chief of security Donald Pierce, and his enforcers, the Reavers, but Caliban is captured and forced to use his powers to track them. Logan and Xavier learn that Laura is one of several mutant children Transigen was breeding using DNA samples from several mutants for the "X-23" project, and that upon completion of the "X-24" project, the children were deemed obsolete and were to be euthanized. Gabriela helped several children escape from the Transigen compound before smuggling Laura, who is revealed to be Logan's biological daughter, across the border.
The Reavers catch up with them in Oklahoma City, but Xavier suffers a seizure and telepathically freezes everyone in their hotel, allowing Logan to kill the attackers before injecting Xavier with a suppressant and escaping. While on the highway, the trio helps farmer Will Munson and his family after a traffic incident. The Munsons invite them over for dinner, and they accept under the guise of being a trigenerational family. When a nearby pipe springs a leak, Logan and Will leave the house to fix it.
While Logan is gone, Xavier recalls a telepathic seizure he had in Westchester, where he inadvertently killed several civilians and X-Men. He expresses his guilt to a person he thinks is Logan, but which is actually X-24, a feral clone of Logan with a limited healing factor. X-24 stabs Xavier through the chest before slaughtering the Munson family. When Logan returns, Xavier succumbs to his wound and Caliban sacrifices himself by setting off two grenades to destroy the Transigen van in which he is being held captive. Logan engages X-24, which gains the upper hand, but Will impales X-24 and shoots it before dying, allowing Logan and Laura to escape.
After burying Xavier, Logan passes out from exhaustion. He wakes up in a clinic that Laura had driven him to, but refuses to get further treatment and wants to abandon the trip. Laura convinces him to complete it, and they arrive at Eden, a safe haven run by Rictor and the other Transigen test subjects that managed to escape. Logan learns that the children plan to journey across the Canadian border and decides to part ways with them. However, when the children are intercepted by the Reavers, Logan intervenes. Dr. Zander Rice, the head of Transigen, pacifies Logan and reveals that the destruction of mutantkind is due to a genetic dampener created by his corporation. Logan shoots Rice dead before Pierce releases a regenerated X-24, who engages Logan. The children wipe out the remaining Reavers before overwhelming and killing Pierce with their powers.
Logan and Laura fight X-24, with Rictor using his seismic powers to help them. However, X-24 brutally impales Logan on the branches of a fallen tree. While X-24 is trying to finish Logan, Laura shoots X-24 dead with an adamantium bullet Logan had been keeping. Fatally wounded, Logan tells Laura not to be the weapon she was made to be before dying in her arms. Laura and the other children mourn his death and hold a somber burial. Laura adjusts the cross on his grave to form an "X" before continuing on their journey across the border in search of a new beginning.
- Princess Celestia, Princess Luna, Knockout, Puffer, Dolphy, Rachel, Mighty Joe, Daylight, Jenny, Pete, Kevin, Dile, Morley, Blitzer, Moon Dancer, Dudley Puppy, Kitty Katswell, Hanah Streaker, Roberta Bravo, SpongeBob SquarePants, Patrick Star, Squidward Tentacles, Sandy Cheeks, Mr. Krabs, Ed, Edd, n Eddy, The Powerpuff Girls (Blossom, Bubbles, and Buttercup), Team Griffin/Eeveelution, The Griffin Family, Vinny Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Little Bear, Duck, Cat, Owl, Hen, Emily, Lucy, Doug Funnie, Skeeter Valentine, Natsu Dragneel, Lucy Heartfilia, Erza Scarlet, Gray Fullbuster, Wendy Marvell, Happy, Carla, Bob the Builder, Scoop, Muck, Dizzy, Roley, Lofty, Spud the Scarecrow, Travis, Tempest Shadow, Grubber, Songbird Serenade, Capper, Captain Celaeno, Princess Skystar, Queen Novo, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, Mitzi, Buttercream Sunday, Sugar Sprinkles, Belle, Ariel, Princess Jasmine, Princess Anna, Elsa the Snow Queen, Mulan, Mushu, Cri-Kee, Pocahontas, Cinderella, Esmeralda, Joy, Sadness, Anger, Fear, Disgust, Judy Hopps, and Nick Wilde guest star in this film.
- Ernie the Giant Chicken, Sideshow Bob, Bobby Briggs, James Woods, New Brian, Trixie, Sunset Shimmer (Oposite), Human Trixie, The Dazzlings, Juniper Montage, Starlight Glimmer, Suri Polomare, Gilda, Lightning Dust, and Madame Pom LeBlanc will work for Donald Pierce in this film.
- The storyline continues in Thomas and Twilight Sparkle meet The New Mutants.