In Dimsdale, Wanda wants to surprise her godson, Jimmy Neutron, with a birthday gift. When she opens the door to Jimmy's room, she discovers that Jimmy is missing, having been abducted by pirates. Outside, Jimmy was actually befriend the Pirate with a Scarf who inexpert in the ways of pirates. To prove himself, Pirate Captain and his crew, the Pirate with a Scarf come across the little boy named Roderick "Rodney" Scott Jones (or refer Scotty whom he called the letter, Number 2). Scotty was actually hail from Grimaborough because of his parents' arguing so he run away. All he has left of his parents is a bear they had given him. When Number 2 returns Jimmy to the palace, Jimmy's god parents are so worried and overprotective they forbid her from be with pirates again.
That night, Number 2 and Scotty helps Jimmy sneaks out of the house to join a festival. A powerful knight named Finn appears and asks Scotty to makes friends with him. When Scotty refuses, Finn furiously tells the Cosmo and Wanda the fate of their "other godson," which surprises Jimmy, Scotty and Number 2 while Pirate Captain and his crew come and tried to warmed him. Finn magically turns everyone including pirates into stone, but Scotty, Number 2 and Jimmy saved by Timmy Turner, a puppet. Finn tells them that he has three days to apologize him, otherwise the spell will be permanent. Timmy takes the gangs to a castle with ocean called the Ocean Kingdom. There Jimmy discovers that "the other godson" of Cosmo and Wanda is Timmy, who was transformed into a puppy by Finn when the latter stole powers from Darlene Paguio, a very powerful hero with special elements after her defeat (explaining why Jimmy's godparents are so overprotective). Scotty and Number 2 decides to build the "Sword of Faith" to break Finn's spell. In order to accomplish this, they must have a measure handle of courage and loyalty, a cloth of love and kindness and a blade of ice lit by hope and peace's eternal flame. The Cloud Queen gives Timmy a crystal bell to ring if she is in need of help.
The group travels to the Forbidden Forest, where they meet a Darlene Paguio who mistakes Number 2 for her enemies and helps them after they get caught in a net. When Number 2 Scotty, his young infant twin siblings, Samuel and Abigail fall into a giant's stew pot, Scotty tricks him into chaining himself to a post, and uses her wooden handle as grappling hook to climb out. The handle is the same length as his, and as a measure handle of courage and loyalty, it turns into a staff for the Sword of Faith. A con artists Miguel and Tulio enters an empty restaurant with three girls, Margo, Edith and Agnes but the chef reveals himself to be a and kills both men and captures the girls. Number 2 Timmy, Jimmy and Scotty comes to the same restaurant, this time apparently filled with people. Scotty sees through the illusion and recognizes them as of the victims, as well as the demon's nine-toothed rake. Darlene bursts into the restaurant and destroys all the corpses, and attacks the chrysalis eater. She captures the demon in her magic bag to turn it into a puppet, but it bursts out of the bag and transforms into a huge boar, collapsing the building. The others retreat and Scotty apologizes Darlene for abandoning her earlier.
That night, the gangs are captured by a gang. It is later revealed to be a ploy orchestrated by Darlene to trick Scotty into befriended with her. Scotty rejects her again, she has him imprisoned. The chrysalis eater reappears and injures Darlene but is chased off by a trio of rivaling demon-hunters. They encountered Sir Slicer, who explains that the hidden clock will turn time back so that humanity never existed. The siblings Kai and Nya comes to their rescues. After Scotty refuses her advances again, Darlene destroys his book of nursery rhymes and he leaves. After trading Number 2's bag of gold for a map from the old man Ferris, the group find themselves in a large cavern filled with gems, where a sign tells them to take only what they need but never from unfaith. Scotty gets one gem but Number 2 gets another; at first Scotty thinks that Number 2 is being greedy but nothing happens. Abby and Sam causes a cave-in thanks to their amazement of the gems' sparkles, which they narrowly manage to escape thanks to her. As Kai starts to forge the Sword, he reveals that he lost all of his money gambling due to his fear of Christmas. He got an extra gem to bring to his parents so that he could get their forgiveness and their protection. Timmy offers his clothing to make the cloth of love and kindness. With all three objects, the "Sword of Faith" is assembled. To prove that the Sword works, Scotty asks for Timmy to be a human from the bottom of the heart. Then, Timmy is transformed back into a human.
Scotty, Jimmy and Timmy return to the Ocean Kingdom on two pegasuses summoned by the Ocean Queen's bell, but Finn pursues them, hurting Timmy. Angrily Scotty gives up and finally agrees to befriended with Finn so he will change Jimmy's godparents and the people back to normal. Finn refuses him because he is hateful, just like his other victims. He takes the Sword from Scotty's hand and causes a snowslide, trapping her. Immediately Number 2 and Darlene comes and helps to dig Scotty out. The others brings an unconscious Scotty to the Ocean Kingdom. After Scotty wakes up, they meet Danny Fenton and Spongebob Squarepants who Jimmy and Timmy used to met them. After Scotty using the Talking teddy bear to learn the location of the clock under the lair, the gangs go to Finn's lair. The girls from earlier that Scotty saves him decides not to give the clouds a dusk color to give Scotty more time after some persuasion by that. While Timmy and Jimmy guards the pegasus, Scotty, Kai, Timmy, and Number 2 slide to the green castle. But Nya is sidelined, and Kai fights against the Ghost man as Number 2 and Scotty searches for the sword. When she finds the sword, suddenly the blade falls. Fortunately, Kai gives Scott his own.
Realizing how to work the sword, Scotty used it to defeat Finn for the love of his family and friends. Finn turns to be an puppet and Sir Slicer tricks Number 2 into removing the seal on his prison and bursts out of the cave, even amputated Scotty's arm. The three demon hunters appear to catch Sir Slicer but he effortlessly kills them. Darlene returns and defends Number 2 and Scotty, but the Sir Slicer mortally injures her. Number 2 admits he loves her, and Sir Slicer proceeds to vaporize her body. Looking at the nursery book again, Scotty realizes Darlene accidentally reassembled the words of his book into those of the Spinjitzu masters that Kai and Nya were actually was. He consults the Talking teddy bear, which says "Say goodbye." He realizes he has to let go of the fear of his parents' arguing to harness his true power. He breaks the clock by dropping the teddy into its gears, then, using his own magic, he blasts Sir Slicer with magic he channels from the clock. He fall and is ultimately erased from existence and the spell on Jimmy's godparents is broken.
Scotty shows them Timmy and Jimmy and the entire family celebrates together, while Kai's parents father forgives him and Nya. Number 2 returns to pirate universe with more confidence, and gets revenge on Black Bellamy and his friends by magically bouncing a basketball on their faces and reunited with his crew. At the end of the day, Scotty got his own infamy as pirates, and the crew present the him with Pirate of the Year trophy. Timmy and Jimmy remarks that they look happy, and gifts the Ocean Queen with the sword, who replies that it will be the first star at night.