- Length- 2:03:47
In Atlantis, the cultures are being reborn after the chaos Dark Cynder caused long ago. Princess Kita is now the Queen, and Milo is the new king. What they think are intruders, are actually Milo's old friends, and the Shell Lodge Squad. The Atlantians greet the heroes, and say there's a problem. The Villain League is after a spear that is considered to be very pure. Kita knows it's the Lost Atlantian Spear, a weapon that is to be given to only the most pure person known. The Lodge knows Kita is the one, and she decides to have Milo and herself go to the surface with the heroes and stop them. Meanwhile, In London, a young Scottish mouse named Olivia Flaversham is celebrating her birthday with her toymaker father, Hiram, until a crippled bat with a peg leg named Fidget, along with Scar, Zira, Shere Khan and Nuka, kidnaps Hiram, and take him to Professor Ratigan who commands him to create a clockwork robot which mimics the Queen of the Mice so Ratigan can rule England. Hiram refuses to take part in the scheme, and Kairi refuses to tell the League who is the bearer of the Spear, whereupon Ratigan orders Fidget, and his two American rat associates, named Abbot and Costello. to capture Olivia, Sora(KH), and SpongeBob so he can feed them to his pet snake, Savio.
Elsewhere, at King Neptune's Castle, Ruber's Griffin steals the Atlantian Spear, and drops it on the ship the Lodge was on after Silverwing attacks him. The Spear lands between SpongeBob and Patrick, and they panic. They soon learn it's the Spear they were looking for after they learn it can make whatever it is used to draw come to life. The Lodge decides to play with it until SpongeBob brings back DoodleBob who steals the spear. They warn the others, and they are unable to try and stop the doodle when they are under attack by a Kraken. The heroes manage to escape the attacked ship, and make it to mainland. Meanwhile, The Vulture Gang battles DoodleBob on the wrecked ship and defeats him. The Vultures then acquire the Atlantian Spear, and fly off to find the Lodgers.
After her dilemma, Olivia searches to find Basil of Baker Street, a world-famous mouse detective who is known to be Ratigan's arch-nemesis, but she can't seem to find Baker St. anywhere. Returning to London after a tour of duty in Afghanistan, Dr. David Q. Dawson stumbles upon Olivia, and helps her find Basil's residence, and some time, they met the Lodge. As they wait for Basil, they suddenly come across a crazed maniac, who actually turns out to be Basil. Olivia tries to tell Basil about her problem, but he doesn't listen, for he was busy doing an experiment on shooting an unknown target. His experiment proves he missed the target, and he curses. Olivia then tells him that she's alone. At first, Basil is reluctant, but when Olivia mentions Fidget, and Scar, Zira, Nuka and Shere Khan, Basil realizes his chance to capture Ratigan.
Meanwhile, the Atlantian Alliance goes after the Kraken. As the team battles the cephalopod, they realize that the Kraken has mind-controlled Vinny into attacking the crew members. Kida figures out that the Kraken is a Darkspawn monster sent by Malefor to help the League retrieve the Atlantian Spear. As the crew is failing, Hiccup and Toothless appear and blast the Kraken dead.
Back on Baker Street, Basil and Dawson take Toby, Sherlock Holmes' pet dog, to track Fidget's scent, until Simba arrives on the scene and tells SpongeBob that the Hyenas are traitors within their ranks. SpongeBob laughs at this until the Hyenas tell him that they're actually antiheroes since they do villainy in Simba, Timon, and Pumbaa's Adventures. Simba tags along with the Lodge to keep an eye on them. The team tracks Fidget at a toyshop where the Atlantian Alliance, Hiccup's team, and The Lodgers that were with them were waiting for them. Basil discovers that Fidget has been stealing clockwork mechanisms and toy soldiers' uniforms. Fidget later traps Olivia, Sora and SpongeBob by ambushing them from inside a toy cradle. Basil and Dawson pursue Fidget, but they aren't going too well. But luckily, Tootless captures Fidget and the rats. After hearing this, Ratigan barely has a heart attack. Zira then decides to change plans. They decide to have Ruber's Griffin find the Vultures that have the Spear, steal it, and bring it back to the League. And if that fails, they will be forced to do a full-scale invasion on the Queen's Palace. And Ratigan reveals that he has a suprise for the Dragon Crew.
While searching the shop, Dawson discovered Fidget's checklist, to which Basil does some chemical tests to discover the list came from the riverfront near the Thames. Shere Khan and the League find out that Scar has left due to the presence of Simba, where Lucky and the other vultures appeared. Lucky gloted about The Shell Lodge Squad looking for the Spear, which they happend to have. Shere Khan, Zira, and Nuka mauled Lucky, while the other vultures flew off with the spear to find and warn the Lodge, with the Griffin in pursuit, but was chased off. Zira and Nuka see this, and decide to invade the Queen's Palace theirselves.
After Fidget (now unexplainly reformed) leads the Lodge and allies to Ratigan's lair, they find that it's deserted. Fidget realizes that the League has planned a full-scale invasion on the Queen's Palace, and Olivia is reunited with her father. This causes Stoick, Hiccup's father, to start an attack on the Villain League before they could invade Buckingham Palace. Hiccup tells his father that Banzai had smelled a dragon that was, what Banzai described, large. Of course this means Ratigan has somehow tamed a Red Death. Stoick decides to attack even though the Red Death is too dangerous for the vikings to handle. Hiccup was concerned about how he fried the Kraken, and about his cowardice. Then he realized it was the right thing to do, and decided to once again plan something stupid.
In Buckingham Palace, the Villain League began their attack, and the vikings and Lodgers were on their way to battle. The vikings were suprised by the Red Death being bigger and stronger than the last one. The Red Death overwhelmed the vikings while the Atlantian Alliance and the Lodgers battled the Villain League War Balloon army. The Red Death was attacked by Hiccup and the Dragon Crew. Hiccup and Toothless blast at the Red Death, forcing it to deal death in the sky. Ratigan was riding on the Red Death's head. Hiccup and Toothless then camouflage theirselves in the dark clouds. As they render theirselves invisible to Ratigan and the Red Death, they repeatedly fire balls of fire at the Red Death. The Red Death blows fire all over the sky, and burns the tail control on Toothless. The duo then dive down toward the ground to try to attack the Red Death's vulnerable trachea.
Basil jumps on to the monster dragon to confront Ratigan. Toothless fires at the Red Death's trachaea, causing him to crash straight into the Big Ben, much to Icky's amazment it still standed even after the explosion. Inside the clock, Basil and Fidget rescue Olivia and safely deliver her to Hiram. Crane flies Fidget to safety while Basil falls of the ledge after a Feral Ratigan grabs him. They both land on the clock's hands, where they are at a very high altitude. Ratigan ambushes Basil, and starts wounding him. Basil is clawed off the ledge of the clock's hand, and Ratigan is about to slash him off. But Toothless saves him by roaring at Ratigan, causing him to fall off the ledge of the clock, and Ratigan falls to the ground far below to his death, catching hold of Basil and dragging him down. Basil keeps hold of the sattle's severed propeller, however, and uses it to save himself.
Back at Baker Street, Basil and Dawson recount their adventures, as well as the queen's gratitude for saving her life. Afterwards, Kita, uses the spear to raise Atlantis back from the shadows of the under-sea cavern, leading Atlantis to offer it's knowledge to the United Universes, and get some tourism. Hiccup, Toothless and the Dragon Crew take Kairi back to the temple, while Fidget gets a note. The note is from L.B. Mammoth of Mammoth Studios in Hollywood who is inviting the Shell Lodge to come to his studio and turn their triumph in Camelot into a movie. But Shifu, the Furious Five, and Po stay behind to guard Atlantis for the moment.
- To Ratigan- By Ratigan and his minions.
- Toxic Love- By Savio
- Circle of Life- Ending song
- Be Prepared- By Scar
- Savio sings Hexxus' song 'Toxic Love' from Ferngully when he eats Ratigan's minion. But Savio is only a boa constrictor, so he is not poisonous in any way, giving no explanation of loving toxics or being locked in a tree like Hexxus was what so ever.
- In the original film, Fidget successfully escapes the toy store with Olivia. But in this version, Toothless captures Fidget, Abbott and Costello. This is because supervideomaniac did not want the star of the show kidnapped. This is what led up to Fidget joining the Shell Louge Squad.