In ancient China, Qin Shi Huang, a brutal and tyrannical warlord, unites the country's kingdoms into an empire and becomes the Dragon Emperor. He orders the construction of the Great Wall of China to bury and curse his dead enemies. The Emperor soon grows fearful that his death will end all he has accomplished and summons Zi Yuan, a sorceress who is said to know the secret of immortality. She seemingly casts a spell on the Emperor in Sanskrit, before he executes General Ming, his trusted friend and Zi Yuan's lover. But foreseeing such events, Zi Yuan immolates and detains the Emperor, transforming his army into the Terracotta Army, and flees.
In 1946, Alex O'Connell, Rick and Evelyn O'Connell's son (along with our heroes), and his archaeology professor Roger Wilson locates the Emperor's tomb.
Meanwhile, the Villains are planing for one last counter attack. While O'Diesel herself is looking over some plans she had written a while back as
Though attacked by a mysterious woman, they succeed in bringing the coffin to Shanghai. Meanwhile, the British government entrusts the O'Connells to take the Eye of Shangri-La back to China. However, they learn that Wilson works for a rogue military faction led by General Yang [whom Bradey O'Diesel and the other villains work for], who had provided the financial backing of Alex's expedition. Yang plans to resurrect the Emperor using the Eye, which contains the Elixer of Life. Then when Savage tells some of the Terminator Battle droids to kill our heroes they are stopped bye Team Griffin/Eeveelution and some of the other heroes from their prievous adventures with the O'Connell's. They open the tomb but accidentally lands on the carriage driver statue, actually revealed to be the Emperor's mummified body. He accepts Yang's service but kills Wilson and escapes.
After the chase, our heroes explain to the O'Connells about the villains, while Willy is thinking about Darth Megadon and hopes of bringing him back to the Lightside of the Force. However Rarity has doubts about Megadon returning to the Jedi's side since he hurt Penny Ling in the previous duel (from Thomas and Twilight Sparkle's Adventures of Sozin's Comet) but Willy states that he felt Megadon feel bad for doing so, but Rarity inadvertently shares her thoughts that Megadon couldn't possible have good in him which puts Willy in his rage mode and he Force Chokes Rarity and angrily states that he can bring his grandfather back to the Light Side, before he realizes what he's doing, and he lets Rarity go before heading out to the back. At first the team are shocked at Willy's actions but then Penny Ling reminds them that Willy's family was killed years ago, but now that he's found one member that is alive he doesn't want to lose him like he lost the rest of his pod.
Willy then ponders about the issue in which he visited by his Father in spirit as well as Annabelle, and he shares about what he did to Rarity and then about his plan to bring Megadon back to the Light Side.
Along with Evelyn's brother Jonathan Carnahan, the O'Connells and the mysterious woman, Lin, travel to a stupa in the Himalayas that will reveal the path to Shangri-La when the Eye is placed on top of it. Meanwhile, Willy and Dolphy get into an argument after Dolphy accidentally asks Willy if he, his family, and Megadon's life have a purpose. And then it ends when Dolphy states to Willy he's starting to sound like Ben Solo before he turn into Kylo Ren, with only Willy telling him that he can just show up and tell him how to live with his life and has no idea what he's been through. With the help of Yetis summoned by Lin, the group hold off Yang's soldiers but the Emperor discovers Shangri-La's location.
Discord then engages with Willy in a Lightsaber duel, Sunil then tries to help Willy out, but is not quick enough as Willy is killed! Fluttershy then races in and Willy then hands Fluttershy his watch as he then fades away. But Megadon then scolds Discord for his deed. As Fluttershy, Penny, and Sunil move Willy out into the open, Skystar races over and is immediately brought to tears
Alex attempts to trigger an avalanche. The Emperor throws a dagger at him, but Rick shoves Alex and is stabbed instead. While Thomas, Twilight, Cadance, Shining Armor, Novo, Barret, Celestia, and Luna failed to notice Megatron is about to blast them. But Percy shoves them out of the way and saves their lives, but is hit by Megatron's blast instead. Lin takes the group to Shangri-La, where Zi Yuan still lives and heals Rick's wound and fixes Percy's boiler. The group discovers that Lin is Zi Yuan's daughter, both rendered immortal due to the power of Shangri-La's waters. As Rick heals, Alex and Lin have grown attached to each other, but Lin refuses due to her immortality; unable to bear falling in love with Alex only to watch him grow old and die, just as Zi Yuan mourned for General Ming.
Meanwhile, Fluttershy is having doubts. As she worries for Willy the spirit of Annabelle and Stoick show up, and give her some encouragement, but she still has some doubt, at the same time, Skystar is still weeping over the loss of Willy, in which Dolphy comes over and asks Novo if he can talk to Skystar in private, as Novo allows him to do so. After moving away from the team, Dolphy then asks Skystar what is up, as she tries to bush it off but Dolphy is not convinced and calmly tells her that he's not trying to interrogate her he's just trying to help her out. Skystar then tells Dolphy she has a secret and doesn't want him to tell anyone about it, as she confesses she's in love with Willy. Dolphy is at first gobsmacked but then he then tells her he feels guilty and awful of saying those things to him. And Skystar asks him what things, as Dolphy tells her that while she and the others were asleep, he and Willy got in a argument about Mgeadon.
And the rest of the gang ponder over the matter at stake, as some of them wish that they had another Jedi that could help them, and then out from the shadows appears what appears to be Ahsoka Tano as Sunil hides under Pepper's tail, believing it's a ghost but intact it really is Ahsoka Tano! And with her is Ezra Bridger, Sabine Wren, Hera Syndulla, Chopper, Zeb, and Captain Rex! And everyone is please to see them, and Ahsoka brought an old friend to Princess Luna. It was Snowdrop! Ahsoka explain she read to history of Luna before she turn into Nightmare Moon, and brought back Snowdrop here at Shangri-La. And Rainbow asks Hera where Jacen is. Hera tells him that Jacen has his own life ahead of him, and now he's a skilled pilot.
Then, the Ed's, Thomas, Twilight, Theodore, Brian, and Sylveon talk that how they will be able to win. Then suddenly the spirit of Yoda appears! And Yoda warmly greets the Ed's, and then Yoda asks why they look so miserable. And Theodore explains that Bradey's getting more powerful with the villains with her, and Brian tells Yoda that they need his help to defeat Bradey and the villains. But Yoda can't help them, because it is something they must do alone. But Eddy asks him how will they defeat her. Yoda tells them: "Use your heart, and defeat her, you will" and he fades away.
The Emperor and General Yang eventually arrive and attack them in Shangri-La, and the Emperor bathes in the mystical waters, which restores his human form and youth, and gives him the ability to shapeshift. Transforming into a dragon, the Emperor kidnaps Lin he flies back to the tomb, raising the Emperor's Terracota Army, planning to cross the Great Wall, where they will be invincible. And then, the Eeveelutions show that they have contacted the Avengers, Guardians of the Galaxy, Godzilla, Lady, the Teenage Mutant Ninja Turtles, and the Justice League for help, including Deadpool, much to the team's dismay. The O'Connells and Zi Yuan pursue the Emperor to the Great Wall where she sacrifices her and Lin's immortality to create an undead army from beneath The Great Wall, led by a revived General Ming. And soon, out of the sky comes Skipper Riley, The Wonderbolts and the Millennium Falcon! As Alex rescues Lin, Zi Yuan fights the Emperor, where she is mortally wounded but secures the dagger. Zi Yuan gives the dagger to the group before dying as the Emperor goes into the Great Wall to use his elemental powers to negate the undead spell.
Fluttershy then races to the wall and manages to get a douse of the healing waters, and race back to try and bring back Willy, but as she races back, Azula fires a fire blast at her, which knocks her unconscious, but Katara uses her special water to revive Fluttershy, and then she brings back Willy. Willy then engages into another lightsaber duel with Discord but gains the upper hand and cuts off his lion arm and then uses Discord's own Changling Saber to execute him. Soon enough the rest of our heroes head out to face each of the villains. As Luna, Elsa, and Anna engage in a lightsaber duel with Nightmare Moon and King Sombra. At first, King Sombra almost wins against Luna but Jasmine cuts off his arm as Elsa then stabs Sombra in the chest. But Nightmare Moon Force Lightning zaps Luna and Elsa and then Force throws them against the wall and then makes a platform pin them down. Anna then battles Nightmare Moon and then cuts off her hooves and then Force grabs one of her own lightsabers and then decapitates Nightmare Moon. While Hiro sends Cerberus down a hill to his doom. Chrysalis then engages in a Lightsaber duel with Belle and Jasmine. As they duel the queen, Cinderella cuts in and overwhelms the Queen, and then finally defeats her.
Then Morack tries to get some of the team using one of the droid tanks but Steam Mech cuts the hydraulic pips on it, making it stop, and then Steam Driller drills onto the side of the driver's cab and then breaks through and kills him as he yells: "SCREW YOU!!!!". Then Starscream appears and firing missiles and his guns at the team, but then Rainbow commandeers a tank and drives it head on towards Starscream. As the F-22 jet and Tank continue driving straight for each other, they both fire at each other and then they both collide as Rainbow fire the turret, which blows up Starscream!
Katara and Zuko then face Azula and just as Zuko is on the verge of defeating Azula, she shoots a bolt of lightning at Katara instead of Zuko. Zuko throws himself in front of her and intercepts the lightning, preventing Katara from getting hurt, but he gravely injures himself after he fails to correctly redirect the lightning. Zuko lies on the ground twitching as Katara and Azula fight. After several minutes of running and being unable to gain the advantage at first, Katara freezes Azula and chains her to the ground defeating her. Katara then uses her waterbending to revive and heal Zuko. As a result of her defeat by two people she considers less than worthless, Azula's mind finally snaps and she screams and sobs in fury, breathing blue fire out of her mouth, yet unable to escape her chains.
Then Blythe and Jenny meet up with Sargeant Savage as he then deploys all 6 of his Lightsabers and engages them in a duel as the Pets and Judy then join in, and manage to disarm him of his sabers, so then Savage then chose to flee on his wheel-cycle. But The group hopped on the backs of the raptors and gave chase. But as they jumped onto the lower level, Judy loses her Lightsaber in which it lands at the feet of Bellwether (as Bellwether takes it for herself). As the group continue to chase Savage, he then drew an Electrostaff and jabbed at them, but Judy manages to grab it and attempts to destroy the main wheel of the wheel-cycle, before the group jump onto it. As they fight with Savage he then draws his blaster pistol and tries to shoot them, but the action makes the wheel-cycle lost control and skid over a cliff side and falls into a pit, as Savage tries to shoot the group with his Blaster, Judy manages to knock it out of his grip with the staff, in which they engage Savage in a hand-to-hand combat. Then Jenny manages to pry Savage's chest plates exposing his spark, but Savage knocks her down as Judy kicks him in the shin, but it does little effect, as Savage then throws Judy asside and then fights Blythe and before he can kill her with the Electrostaff, Judy Force grabs Savage's blaster and shoots his spark. Then Blythe, Jenny, and the Pets all fire their blasters at Savage's spark, which then caught fire, incinerating his internal components, killing him.
But then as the group return to the main battle Bellwether appears before them and draws her Lightsaber. As Judy then borrows Buttercream's Lightsaber/Blaster and duels Bellwether alternating from Lightsaber Blade action and Blaster fire. As Buttercream retrieves Judy's Lightsaber from Bellwether and joins the duel. As the duel rages on, Bellwether throws her Lightsaber at Buttercream, seemingly killing her. But then Judy Force grabs her own Lightsaber and continues to duel Bellwether using her and Buttercream's Lightsaber. She then tells Bellwether that she was right about fear being a powerfully motivator but that states the Force is far stronger than fear. as she then destroys Bellwether's lightsaber and the broken saber falls into a lava river. Bellwether then dangles from ledge but she loses her grip and falls into the river. As Buttercream walks over.
Meanwhile the Crusaders, Blythe, the Pets, Hanah, Roberta, and Jenny engage Diamond Tiara, Silver Spoon, The Biskit Twins, Cashmere and Velvet, Biff and Tiff in a duel
Then Rambo sneaks up to one of the droids, and decapitates it and takes over it, and kills a large number of it with help from Peter and the guys. And then X-Wings appear as the Resistance has been called for help. And soon they deal with a large number of Terminator Battle Droids.
At the same time, Twilight has engaged both Trixie and Starlight but they cheat and make Twilight lose her ground but before they can kill her, Ahsoka walks over and ignites her own sabers. As Trixie (recognizing Ahsoka all the way from the Clone Wars) is gobsmacked as Starlight is confused of the matter. As Trixie states that Ahsoka can't be alive as Ahsoka claims she is, as she engages both Unicorns
Rick and Alex fight off the Emperor while Evelyn and Lin fight and kill Yang. The Emperor gains the upper hand over Rick, but Rick and Alex manage to stab the Emperor with the dagger, killing him and defeating the Terracotta Army. Ming's army briefly celebrates before finally moving on to a peaceful afterlife. But suddenly a second wave of Changelings, the Indominus Rex and Spino show up! But then suddenly, King Kong appears! Then he battles the living daylights out of the bad dinosaurs. And our heroes charge to the Changeling army to buy the others time to save Megadon and defeat Bradey.
Willy then goes to confront Megadon, hoping to free him, as he battles him in a Lightsaber duel as HIM watches in the background. Willy says the conflict is in him but Megadon claims he has no conflict and he throws one of his Lighterangs at the walkway with Willy on it, and then after Willy falls down, he then searches for him as he feels Willy's feelings where he finds out about Dolphy being his cousin, And claims that if he won't turn to the Dark Side, then maybe Dolphy will, but Willy in his rage mode, then jumps out from the shadows. He then battles Megadon furiously and then as he clashes his saber against Megadon's at fast speeds and then he cuts off Megadon's own fin! HIM then tells him to strike him down and take his place, but Willy then notices that Megadon's fin is actually a robotic one and then he looks at his own fin, and realizes what he's doing as he snaps out of his rage mode and deactivates his saber. And then claims he is a Jedi.
Returning to the rest of the gang, they are continuing to kill off more Changlings as Kitty is dueling Katty. But it turns out to be too much for our heroes, as Katty calls for them that they've thought bravely. But tells them to surrender and their lives will be spared, but Kitty refuses for them to be hostages. Katty responds for the Changelings to kill them, but then there was a rumbling sound. And Sunil hides in Pepper's tail believing it's an earthquake, but Hanah looks over to the side and shouts: "LOOK!". And there charging at the Changeling army was every single prehistoric animal (including the dinosaurs in Jurassic Park) and they take down a huge wave of them. And Kitty tells them to charge again and they did and begin over running Changeling army.
HIM then angrily starts Force Lightning shocking Willy! As he does, Willy calls out to Megadon to help him, but as HIM continues shocking him, he Megadon looks between the 2, and then HIM pauses for a moment and then claims Willy will now die as he resumes Force Lightning shocking Willy, as he yells in agony. But then Megadon grabs HIM and then as he's being shocked by HIM he then throws HIM over the cliffside and HIM falls into a lava river and is killed. As Willy then helps a very weak Megadon up.
As T.C. and Hugs confront Bradey O'Diesel where they duel her to the death but due to Brandy now having machine-phase matter within, the duel proves to be difficult
The O'Connells return to Shanghai while Jonathan decides to move to Peru with the Eye of Shangri-La, as he wants to go somewhere with no mummies. However, in postscript, it is revealed that upon his arrival, mummies were discovered in Peru.
- The Powerpuff Girls (Blossom, Bubbles, and Buttercup), Courage the Cowardly Dog, Norbert and Dagget, Samurai Jack, Rodney Copperbottom, Fender Pinwheeler, Wonderbot, Piper Pinwheeler, Crank Casey, Lug, Diesel, Hiccup, Toothless, Astrid, Stormfly, Snotlout, Hookfang, Fishlegs, Meatlug, Ruffnut and Tuffnut, Barf and Belch, Valka, Cloudjumper, Eret, Skullcrusher, Gobber, Grump, Thomas, Twilight Sparkle, Percy, Pinkie Pie, Toby, Applejack, James, Rarity, Gordon, Rainbow Dash, Henry, Fluttershy, Edward, Emily, Hiro, Charlie, The Logging Locos (Bash, Dash and Ferdinand), Spike, The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo), Button Mash, Babs Seed, Skarloey, Rheneas, Sir Handel, Peter Sam, Rusty, Duncan, Luke, Shining Armor, Princess Cadance, Bill and Ben, Bertie, Terence, Stephen, Theodore Tugboat, Hank, Emily, George, Foduck, Spencer, Duck, Donald and Douglas, Oliver, Toad, Arthur, Murdoch, Daisy, Ryan, Skiff, Ashima, Victor, Kevin, Zecora, Coco Pommel, Cheese Sandwich, Zephyr Breeze, Maud Pie, Limestone Pie, Marble Pie, Big Macintosh, Braeburn, Little Strongheart, Princess Ember, Gabby, Big Grizz, Steamy, Puffy, Evan, Shai-Shay, Rodger the logging loco, Rattlesnake Jake, 1206, Socky, Skunky, J.J., Buzz, Mako, Shema, Sharky, Willy, Mr. Great White, The Miner Trains, The Planet Trains, T.C., Hugs, Sherin, Marshall P.F., General Dedrich, The Trolley Fighters, Timber, Splinter, Chomper, Whiffle, Falcon, R3-X3 (Rax), Judy Hopps, Nick Wilde, Dusty Crophopper, Ishani, The CyberSquad (Matt, Jackie, Inez, and Digit), Wreck-It Ralph, Vanellope von Schweetz, Fix-It Felix, Jr., Sergeant Calhoun, Belle, Ariel, Melody, Princess Jasmine, Jenny Foxworth, Princess Anna, Queen Elsa, Merida, Mulan, Mushu, Criki, Pocahontas, Esmeralda, Snow White, Princess Aurora/Briar Rose, Alice, Mordecai, Rigby, Benson, Skips, Pops, Muscle Man, Hi-Five Ghost, Margaret, Eileen, Knockout, Puffer, Dolphy, Rachel, Mighty Joe, Daylight, Jenny, Pete, Kevin, Alberto, Morley, Blitzer, Dile, July, BZ-7 (Buzz), R5-K5 (Kratt), Team Chugger, Tillie, Chip, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, Gail Trent, Mitzi, Buttercream Sunday, Sugar Sprinkles, Captain Cuddles, Eliza Thornberry, Darwin, Spongebob, Squidward, Sandy, Patrick, Mr. Krabs, Blackie, Wilbur, Cardigan, Templeton, Joy, Aranea, Nellie, Aang, Katara, Sokka, Toph, Zuko, Iroh, Suki, Mai, Tylee, Appa, Momo, Jenny Wakeman, Danny Phantom, Dudley Puppy, Kitty Katswell, Hanah Streaker, Roberta Bravo, Invader Zim, Gir, Princess Celestia, Barret Barricade, Princess Luna, Princess Sharon, Princess Sunlight, Princess Skyla, The Crystal Crusaders, Princess Yuna, Moon Starlight, Zenorita Cebra, Tempest Shadow, Grubber, Songbird Serenade, Capper, Captain Celaeno, Princess Skystar, Queen Novo, Jimmy Neutron, Godard, Carl Wheezer, Sheen, Cindy Vortex, Libby, Timmy Turner, Cosmo, Wanda, Lightning McQueen, Mater, Cruz Ramirez, John Rambo, Team Griffin/Eeveelution, The Griffin Family, Vinny Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Nightstriker, Breon, Selena, Alan, Little Bear, Duck, Cat, Owl, Hen, Emily, Lucy, Doug Funnie, Skeeter Valentine, Roger Smith, Bender Bending Rodríguez, Minerva Mink, Master Shake, Meatwad, Frylock, Pazu, Sheeta, The Dola Gang, The Crystal Prep Girls, Wubbzy, Widget, Walden, Daizy, The Young Six, Natsu Dragneel, Lucy Heartfilia, Gray Fullbuster, Erza Scarlet, Wendy Marvell, Happy, Carla, Sunset Shimmer, the Human Mane 5, Sci-Twi, Spike the Dog, Inspector Gadget, Coloratura, Moon Dancer, Derpy Hooves, Dinky Hooves, Octavia Melody, Vinyl Scratch, Lyra Heartstrings, Bon Bon, Optimus Prime, Bumblebee, Ironhide, Ratchet, Sideswipe, Dino, Jazz, Skips & Mudflap, the Wreckers, Hound, Cross-Hairs, Drift, Hot Rod, Cogman, Wheelie, Brains. the Dinobots, and Dragonstorm guest star in this film.
- Bradey O'Diesel, Mojo Jojo, The Rowdyruff Boys, Le Quack, Katz, Big Toe, HIM, Phineas T. Ratchet, Madame Gasket, the Indominus Rex, Spino, the Indoraptor, Sailor John, Drago, Drago's Bewilderbeast, Muska, Rourke, Helga Sinclair, Diesel 10, Diesel, Splatter and Dodge, Discord, Ripslinger, Ned and Zed, Nightmare Moon, King Sombra, The Nightmare Train, The Evil Mane 6, Trixie, Suri Polomare, Madame Pom LeBlanc, Gilda, Lightning Dust, Starlight Glimmer, Dr. Claw, Diamond Tiara, Silver Spoon, The Biskit Twins, Cashmere and Velvet, Biff and Tiff, Sargent Savage, DOOM, The Chameleon, Morack, Kara, Plankton, Karen, Azula, Katty Katswell, Vicky, Crocker, Dawn Bellwether, Megatron, Darth Megadon, Starscream, Shockwave, Soundwave, Hacker, Buzz and Delete, Plankton, and DoodleBob will work for Gin Shi Huang in this film.
- The Avengers, Bucky Barnes, War Machine, Falcon, Black Panther, Ant-Man, Doctor Strange, Spider-Man (Tom Holland version), Teenage Mutant Ninja Turtles, the Justice League, Deadpool, Lady, Godzilla, King Kong, and some special guest stars make climax appearances in this film.
- A special friend of Princess Luna will return in this film.
- Darth Megadon reforms in this film and his true face is revealed.
- King Kong, Jurassic World, Jurassic Park III, and The Mummy: Tomb of the Dragon Emperor are Universal films.
- The story of the Dragon Emperor
- 1946/fly fishing
- The dig site
- Bradey's plan/"In The Dark Of The Night"
- Johnathan's Nightclub
- General Yang's army camp
- The Dragon Emperor awakes/The chase
- Back at the bar/explanations
- Arriving at the Himalayas/making camp
- Alex and Lin talk
- Rick and Alex compare their guns
- Battle against the villains and Yang's soldiers
- Willy's death
- Rick saves Alex/Percy saves Thomas, Twilight, and the royals
- In Shangri-La/The new plan of attack
- Fluttershy's doubts/return of an old friend
- Yoda appears!
- The Emeperor regains his power
- Welcome to the 20th Century!
- Willy's ressurection
- Willy vs. Discord
- Defeat of some of the villains
- Yang and Choi's death
- Optimus vs. Megatron
- Death of the Emeperor
- Second wave of Changelings!
- Willy's Duel with Darth Megadon: Final Round
- Bradey's demise
- Ending/Back to Patchy
- Thomas and the Magic Railroad - Diesel 10 & Splodge (when Bradey and the heroes prepare for one more counter attack)
- In the Dark of the Night - Bradey O'Diesel
- Star Wars Episode II: Attack of the Clones - Chase Through Coruscant (during the chase through the streets of China)
- Star Wars Episode I: The Phantom Menace - Qui Gon's Noble End (when Willy is killed by Discord)
- Thomas & Friends - Avalanche Theme (when the avalanche happens)
- Sometimes I Wonder - Fluttershy
- Treasure Planet - Silver Comforts Jim (when Stoick and Annabelle comfort Fluttershy)
- Star Wars Episode II: Attack of the Clones - Love Pledge and the Arena
- Pokémon Ranger and the Temple of the Sea - Sinking Temple (when the second wave of Changelings fly in)
- Star Wars Episode VI: Return of the Jedi - Victory Celebration
- Ocean Man (end credits)
- Locomotion (end credits)
- A Friend for Life (end credits)
- How To Train Your Dragon - Test Flight (end credits)
- Wherever the Trail May Lead (end credits)
- Anytime You Need a Friend (end credits)
- Pirates of the Carribean - Two Hornpipes (end credits)