A young boy ventures into an old relic shop, where he meets its mysterious owner, Mr. Liu, who begins to tell the boy the legend of Ninjago. Ninjago is a city that is frequently attacked by the evil Lord Garmadon, who is the father of Lloyd Garmadon and husband of Koko. The city despises Lloyd for this relationship, which puts Lloyd in emotional stress. They do not know that Lloyd is part of the Secret Ninja Force, consisting of Nya, Zane, Jay, Cole, Kai and their master, Master Wu, who always stop Garmadon from taking over the city. On Lloyd's birthday Garmadon attacks the city once again, only to be defeated. He escapes and throws many of his generals out the volcano for failing to help him. He then beings to form a big attack to conquer Ninjago, and decides to build a gigantic mech that is immune to weapons.
Meanwhile, Lloyd and his friends see the return of Master Wu, back from his long trip. Master Wu tells them they aren't real ninjas if they use only mechs and machines. He discusses with the Ninja of their respective powers: Nya's power over water, Kai's power of fire, Jay's power over lightning, Cole's power over earth, and Zane's power over ice. Wu then states that Lloyd is the green element, only to be confusing Loyd with that topic. Master Wu tells Lloyd he must not be angry at Garmadon; he must use his mind to fight. Wu mentions an Ultimate Weapon, giving Lloyd an idea to finally defeat Garmadon once and for all, despite being forbidden to use it. The next day Garmadon attacks the city with his giant mech. He successfully defeats Lloyd and his own mech. As Garmadon declares his rule over Ninjago, Lloyd returns with the Ultimate Weapon. He fires it, revealing it to be a laser that attracts a real-life cat named Meowthra. Meowthra starts destroying the city, while trying to get the laser. Garmadon points the laser to make the cat destroy the other mechs, before Lloyd breaks it. As Garmadon celebrates his victory, Lloyd reveals that he is the green ninja, and tells Garmadon that he wishes he wasn't his father, leaving Garmadon speechless.
Lloyd meets up with his friends and Master Wu, who are all upset with him for using the weapon. Wu tells them they must use an Ultimate Ultimate Weapon to stop Meowthra from destroying the city, which they would reach by crossing the Forest of Dangers, the Canyon of Death, and the Temple of Fragile Foundations. Garmadon overhears Wu talking about the weapon and follows close behind. He meets up with Wu and fights him, only to end up in a cage, defeated. However, Wu loses his balance and falls off a bridge into a river, telling Lloyd he must use inner peace before getting swept away. The ninjas decide to continue on, with Garmadon leading them much to Lloyd's disappointment. They are caught by Garmadon's former generals, who want revenge. The ninjas try to fight but are easily defeated; they retreat leaving Lloyd and Garmadon behind to be caught by the generals. The generals begin to fire Lloyd and Garmadon into a volcano, however the rest of the Ninja save the day using stealth fighting. They all work together with Garmadon to escape the angry generals by building a makeshift helicopter, and Lloyd and Garmadon bond together in the process.
They eventually crash down onto the Temple of Fragile Foundations. Garmadon reveals that it is his home, as well as revealing to Lloyd that Koko formerly being a ninja warrior herself, her cover name being The Lady Iron Dragon, Nya's idol. He reveals to Lloyd that he wishes he had stayed with him and his mom after deciding to conquer Ninjago, but he couldn't change so he had to stay behind. The ninjas find the Ultimate Ultimate Weapon, consisting of a set of trinkets, only to have it stolen by Garmadon who still wants to take over the city. He wants Lloyd to be his general, but Lloyd rejects his offer. Out of fury, Garmadon locks all of them in the temple as it begins to collapse. Lloyd realizes that inner peace means for them to unleash their power within, and they successfully do this, escaping from the collapsing temple. As they fall of a cliff, Wu saves them with his ship, and they head towards Ninjago. Garmadon arrives and tries to control Meowthra with the weapons but Meowthra eats Garmadon instead. Lloyd and the crew arrive and begin fighting Garmadon's army. As Lloyd approaches Meowthra, he reveals to everyone that he is the green ninja, and realizes that green means life, which brings everything together. He comforts Meowthra, and tells Garmadon he forgives him, and that he's sorry. Garmadon cries tears of fire, which causes Meowthra to spit him out. After reconciling, Garmadon moves in with Lloyd and Koko, Meowthra becomes the mascot of Ninjago, and Lloyd is hailed as a hero. As the story concludes, Mr. Liu tells the boy that he will start to train him as a ninja.