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.
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, Mojo Jojo, The Rowdyruff Boys, Le Quack, Katz, Big Toe, Phineas T. Ratchet, Madame Gasket, the Indominus Rex, Spino, 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, Dr. Claw, Biff and Tiff, Sargent Savage, DOOM, The Chameleon, Morack, Kara, Plankton, Karen, Azula, Megatron, Darth Megadon, Starscream, Shockwave, Soundwave, Hacker, Buzz and Delete, Plankton, and DoodleBob 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. They open it 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 Ozin'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. 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.
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, 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, 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
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. 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. 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
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
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 the Indominus Rex and Spino show up! But then suddenly, King Kong appears! Then he battles the living daylights out of the bad dinosaurs.
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.
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, 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, Spencer, Duck, Donald and Douglas, Oliver, Toad, Arthur, Murdoch, Daisy, Ryan, Ashima, Victor, Kevin, Zecora, Coco Pommel, Cheese Sandwich, Maud pie, Limestone Pie, Marble Pie, Big Macintosh, Princess Ember, Gabby, Big Grizz, Steamy, Puffy, Evan, Shai-Shay, Rodger the logging loco, Rattlesnake Jake, 1206, Socky, Skunky, J.J., Buzz, Mako, 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, Judy Hopps, Nick Wilde, Sheeta, Pazu, The Dola Gang, Dusty Crophopper, Ishani, The CyberSquad (Matt, Jackie, Inez, and Digit), Wreck-It Ralph, Vanellope von Schweetz, Fix-It Felix, Jr., Sergeant Calhoun, Anna, Elsa, Ariel, Jasmine, Merida, Belle, Team Chugger, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, Gail Trent, Mitzi, Buttercream Sunday, Sugar Sprinkles, Spongebob, Squidward, Sandy, Patrick, Mr. Krabs, Team Chugger, Godzilla, King Kong, 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, Jimmy Neutron, Godard, Carl Wheezer, Sheen, Cindy Vortex, Libby, Timmy Turner, Cosmo, Wanda, Kanan Jarrus, Ezra Bridger, C1-10P (Chopper), Garazeb Orrelios, Sabine Wren, Hera Syndulla, John Rambo, the Human Mane 5, Human Twilight, Inspector Gadget, Optimus Prime, Bumblebee, Ironhide, Ratchet, Sideswipe, Dino and Wheelie 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, 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.
- 2 special guest stars makes a climax appearance 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
- 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
- Kong vs. the Indominus and Spino
- Willy's Duel with Darth Megadon: Final Round
- Bradey's demise
- Ending/Back to Patchy