The Ninja are house hunting. The only house they can afford turns out to be a one-bedroom, one half bath apartment without lighting. Jay and Kai argue they need a better place to train Lloyd and agree to buy an expensive hero suite that's out of their price range. To help pay for this, Zane takes on a job as a professional chef, but then got distracted by news of a bank robbery, he accidentally drops an egg on a Darkley's student and was fired as a result, leaving as his skin to cover the damage during the attack from the Great Devourer started peeling off. While fighting snakes, Zane shows the Ninja that they can use makeshift weapons.
Zane and the other Ninja began to train Lloyd in their apartment, though soon realized their conditions were unsuitable for the task. They set out into the city to search for a better place and soon came upon Grand Sensei Dareth's Mojo Dojo.
Following their first session training Lloyd in the dojo, the Ninja exited to find the city under attack by Captain Soto's pirates. The Ninja quickly boarded a bus and raced towards the boat. After stopping by Wong's Costume to disguise themselves as pirates, Zane and the others boarded the ship and confronted Soto's crew. After a brief fight and with the help of the Ninja, the pirates were eventually subdued.
Zane and the Ninja are training Lloyd in Dareth's Dojo, but Lloyd can't get the hang of it. Nya enters and hands Master Wu a note to Lloyd from his old school saying that there is going to be a ceremony, and they want to give Lloyd an honorary degree of excellence.The Ninja ride the Ultra Dragon to the school, and discover that they've changed from being a boarding school for bad boys, to a school for "great children." When they enter the school, they find that there are no teachers around. They encounter one of Lloyd's old classmates "Gene", who knocks out the other Ninja and take Lloyd captive. The four ninja wake up locked in a room with the teachers, who reveal that the children locked them in there, and lured Lloyd there to make him their leader. Zane activates his "battering ram mode" to bust down the door, but it doesn't work. They make several more attempts to escape, but none work. Zane points out that the school was built for evil, so there may be some hidden passageways around. Jay finds a book switch that opens a hidden door, and the ninja escape through it. Zane uses a lightbulb function to make his face glow like a lamp and reveals that there are spiders all around them in the passageway.
While the children are interrogating Lloyd, the Ninja Doppelgängers arrive at the school, and the kids try to fight back, but they're too strong and the Students run away. Zane and the real Ninja arrive and meet the doppelgangers, and attempt to fight, but they are equally too strong, so there is no winner.
Lloyd and the students devise a way to help the Ninja defeat the evil ones. They come out of a classroom, all dressed as Ninja, and help the main four defeat the evil doppelgängers. Their plan works, and the evil ninja are slowly eradicated.
Lloyd is training in Dareth's dojo with Zane the other Ninja balancing on top of him when a wrecking ball smashes through the window and knocks them over. Dareth tells them that a company called Darnagom Enterprises wanted to put a golf course in place of Dareth's dojo, and if he can't come up with 50,000 dollars by tomorrow, the dojo is gone. Zane realizes that Darnagom is an anagram for "Garmadon", and that Garmadon is trying to get rid of his dojo so that Lloyd can't train. Nya interrupts and says that there is a racing competition that's prize is 100,000 dollars, and the Ninja agree they will all enter to help dareth.
The next day, Zane and the other Ninja get in line to race in the Ultra Sonic Raider, and Lloyd is racing with the Ultra Dragon. The race begins, and around the middle, Garmadon crashes the race in the Dark Bounty to try and stop the Ninja from winning. Garmadon drops serpentine on the USR to slow them down while they transfer fuel from Jay's parents ride to theirs. They quickly get rid of the snakes and make a quick addition to the USR, and they race on.
Near the end, it's just them and Garmadon, and they show off the new mode for the USR that allows part of it to fly away, allowing them to win the race just in time. At the finish line, Lloyd takes the Bounty back with them, and Garmadon escapes with Skales.
The Ninja are trying to train Lloyd, however, the latter wasn't interested. When Nya told them about Garmadon's break-in at the Museum, they headed to the Ultra Stealth Raider to stop him. They did stop him from reviving the Grundle, however, when chasing the Serpentine and get back a stolen sarcophagus, they realized they've been turned into kids. When the police arrived, they accused them of the theft.
The Museum Curator explained that the Grundle skeleton was missing. Zane theorizes that the Mega Weapon did work, but the Curator and officers doubted it. They snuck away by disguising themselves in the clothes they stole from other kids. They called the Bounty, asking for Lloyd to meet them at Buddy's Pizza with their weapons. Lloyd told them he knows who can help defeat the Grundle.
The enter the comic book store, where they meet Rufus MacAllister. He explained Ninja weapons are useless against it and that they're nocturnal; an illumisword will do the trick. They must be won in a trivia battle, and they encouraged Lloyd to win it.
Later, Lloyd lost the trivia battle. When the Grundle came, the Ninja tries to open the door, but it's been blocked by the fallen debris. Grabbing the illumiswords, they tried to defeat it, but they easily broke. When Wu gave them tomorrow's tea, the Ninja were reluctant at first to turn Lloyd into a teen. However, Lloyd used it for them, shocking the Ninja when they find him as old as they are.
Zane and the Ninja are training Lloyd in his new, older body on the Bounty. The Falcon comes back and gives news that the serpentine and Garmadon have returned to the Lost City of Oroborus, so they set a course for there.
The Ninja arrive, and Garmadon retreats to a nearby house and wishes he could go back in time and make it so the ninja were never formed in the first place, and he leaves through a time vortex. The Ninja (except Lloyd) follow him in and find themselves on the day that Master Wu found Kai, the day that Nya was taken by Garmadon.
Master Wu tells them that if you change anything, it changes everything. Zane reminds them that if they do anything in the past to alter something in the future, the future would radically change. They see past Wu, and take him to ask him for help stopping Garmadon. He agrees to help protect past Kai as best he can.
Wu goes on with saving past Kai, but Garmadon prevents Samukai from taking Nya. Zane says that no matter what, Wu needs to convince Kai to train and become a ninja, or else Lloyd will never become the Green Ninja. Kai goes with Wu, but he seems disinterested. Zane says that they must follow them to make sure Kai still becomes a ninja.
At the Monastery, the ninja realize that past Kai is totally disinterested in becoming a ninja, so they come up with a plan to kidnap Nya at night, and deliver her to the skeletons so that Kai will get his motivation back. That night, they dress as skeletons, and take Nya, but unfortunately they find their past selves trying to intervene. They get rid of them, and take Nya, thus convincing Kai to become a Ninja.
They follow past Kai into the Fire Temple where he is supposed to take the Fire Sword and save Nya, but this time future Garmadon helps past Garmadon. Zane and the others intervene to help past Kai defeat Garmadon. They realize that everything they've done has so far already drastically altered the future... Zane points out that the only way for them to theoretically erase the events they've altered, would be to destroy the Mega Weapon by using the separated Golden Weapons, as they have equal power. They all use the weapons on the Mega Weapon, causing it, and the Golden Weapons to shoot up into space and explode. Nya and past Kai start to disappear, and the events of the future are set back on track. In the future, they realize that the Mega Weapon had been erased from existence.
The Ninja are woken up early in the morning, with Zane last to get up, for a "sunrise exercise." Master Wu comes in to tell them that the Ultra Dragon made a mess outside, and someone had to clean it. Lloyd is picked to do the cleaning, and after it is done, he laments about how his mother left him at Darkley's when he was young. As he finishes, Nya comes in to tell them they have a mission at the Ninjago Museum.
At the Museum, the curator tells them that the Devourer venom has seeped into the sewers and caused the Stone Warrior dolls to come to life. Zane and the others handle it, and one of the dolls run away. Wu chases after it. After crushing it, he turns around to see Misako, Lloyd's mother. Zane and the others come to see what's going on and they are introduced. Lloyd at first resents her, for abandoning him, and walks away.
Misako and the Ninja follow Lloyd into a room with a large sinkhole in it. Misako goes on to explain the story of the Stone Warriors. She tells the usual story about how the First Spinjitzu Master created Ninjago, but tells the rest of it and how where there is light, there must be shadow. Zane asks if Master knew about this, and he says he did. Misako goes on to say that the Overlord existed to combat the FSM, and created the indestructible Stone Warriors. When the FSM couldn't defeat them, he split Ninjago in two, and on the other half, he exiled the Overlord and his army there and dubbed it the Dark Island.
Meanwhile in another room, the museum curator shows off their newest exhibit, which is a giant Stone Samurai Warrior, which comes to life after a drop of Devourer guts falls on it. The Stone Samurai Warrior barges in on the Ninja. Zane points out that the Devourer's venom awakened him. They attempt to destroy it, but they can't. They run away and escape to a nearby room where they devise a plan for Lloyd to defeat it. Lloyd crawls into an air vent while the Ninja distract the Stone Warrior. Thy drop a skeleton on top of it, and Lloyd lures it into the sinkhole that Misako found earlier.
At Dareth's dojo, Zane and the Ninja are training Lloyd to fight without seeing, when there is an earthquake, that Master describes as something that was not caused naturally. Zane sends his Falcon to look for danger, and find the source of the earthquakes. The quakes start to cause rifts to form in the ground, and a woman falls down a cliff, but the Ninja save her just in time. Misako comes and tells them that in the prophesy, earthquakes would be a warning for something... She also reveals that she found the giant Stone Warrior underground, and suggests there could be more of them there.
Suddenly, the Falcon discovers more Stone Warriors coming from underground. The Ninja attempt to fight back, but the army is indestructible. Master Wu tells them that they have to evacuate the remaining people out of there on the Bounty. Zane and the Ninja go to the rendezvous point and start evacuating people out, all the while fending off Stone Samurai Warriors. When they get to the top, the citizens and the Ninja board the bounty except Misako. They wait for her, but she takes too long so Wu goes after her. Zane and the others fly away, and catch Wu and Misako as they jump out of the building to evade the Stone Warriors.
Zane and the rest of the Ninja sail to an island with a prison tower. When the Ninja get to the top, Dr. Julien greets them and takes them in. Inside he seats them and haves a robot serve them tea. There, Dr. Julien tells Zane what happened after his apparent death. After Dr. Julien turned off Zane's memory switch, he really did pass away, but Samukai revived him with a special elixir in return that he create the Skeleton Army's vehicles. When Dr. Julien refused, Samukai locked him in the prison tower with a Leviathan to keep guard, promising the doctor if he did what he said, he would see Zane again. However, time passed and Dr. Jullien wondered if he'd ever see Zane again.
After he finished telling his story, the Leviathan comes and sends out a tentacle with eyes to check on Dr. Julien, while the others hide. After it goes away, Dr. Julien and the Ninja work together to fix the Bounty's rocket boosters. As the Bounty takes off, the Leviathan grabbed the ship. Zane jumped into the water and freed the creature from its chains using starteeth. Finally freed, the Leviathan lets the Bounty go, and they fly off to the Island of Darkness.
Zane and the Ninja are shoveling dirt and sand onto the Bounty to hide it from the Stone Warrior Scouts. They say they want to fight them, but they are indestructible. Wu mentions that they have to find the Temple of Light. Misako goes on to tell the tale that if they go to the Temple, then they could receive pure elemental powers. They, however, do not know its location, the only thing they have that might help them find it is a medallion. The Ninja head off to find it, with Lloyd staying behind.
Later, at a cliffside, they are looking through the medallion like a spyglass when Zane spots his Falcon at the Stone Warrior camp. He says he needs to get it back, to give to his father to fix. To the dismay of the others, Zane sneaks into the camp and takes it, and in the process, reveals his location to the Stone Warriors. He is backed into a corner, so the others come to help. They escape onto an unstable bridge, and are cornered once again. Zane says he knows how to get them out of the mess, and when the bridge gives way, and the Ninja each grab a wooden plank to ride to safety.
They run back to their base and inform the others that they were spotted, but they found the Temple of Light. Zane's father introduces the vehicles they have built for them. All the Ninja now drive the Earth Driller to the Temple, with the Stone Warriors not too far behind. They get to the base of the mountain, so Kai unpacks his new Fire Mech that all the Ninja ride on. They get to the top and enter the Temple, they find that on the wall are all the events that led up to them finding it. Lloyd goes to the center to strike the bell, and Zane and the other's Elemental Blades appear, along with Lloyd's Golden Dragon. As this happens, the Stone Warriors attack and the Ninja show off their now power, and how they are finally able to defeat them.
The Ninja are on a beach, relaxing and testing out their new powers and "witty quips," when Cole shoots a rock blast at the Falcon. Zane saves it, and says he is glad they are reunited. The Ninja meet with the others, and Misako reveals that there is a way for the Final Battle to be averted, but she needs Ninja help.
Zane and the others dress as Stone Warriors, and escort Misako to the Stone Warrior camp. When they arrive, General Kozu takes Misako to Garmadon, and the Ninja retire behind a rock. A few moments later, Kozu returns, and tells the Ninja that they must help out with the construction of the Ultimate Weapon. They start working on the scaffold, when their identities are revealed, and they flee. They find Misako, who has the Helmet of Shadows, and they escape on the Earth Driller, with Garmadon not too far behind. They are stopped by Garmadon, when Lloyd saves them.
They make it to the Celestial Clock, and look for the pedestal for the helmet. When they are unsuccessful, they are backed off a cliff by the Stone Warriors, who kidnapped Nya. They return back to their base, dismayed at their defeat.
The Ninja get ready to go and fight Garmadon. They get to the camp to find it abandoned, and that the Ultimate Weapon has been taken to the beach. They go there, after fending off an evil Nya, and find that the Overlord has crossed over into their world by possessing Garmadon. Lloyd fights the Overlord, and loses, and the Overlord opens a vortex to Ninjago City and leaves them all on the island.
The Ninja are on the beach of the Dark Island, with no way to Ninjago. They all express their misfortune on that evil has defeated them. Lloyd pep talks them into rejoining the fight. Misako tells them that there may be a way back.
They go back to the Temple of Light, and uncover an old Golden Mech that belonged to the First Spinjitzu Master. Lloyd takes control of it, and with the help of the Ultra Dragon, head back to Ninjago.
When they make it back, they find out that the Overlord has turned everyone evil. Zane notices that the Overlord has completed his transformation, into a large dragon that is perched atop a tower. The Ninja realize they need to get Lloyd up there, so they take him to it, fending off Stone Warriors as they go. They are almost defeated, when Dareth puts on the Helmet of Shadows and controls the Stone Army. Now the Ninja help Lloyd up the tower to the Overlord. One by one, the Ninja are all corrupted by evil until it is just Lloyd left. He gets to the top, and unlocks his Golden Power, and defeats the Overlord.
After he is defeated, Zane and everyone else is turned back normal. Zane awakes with the others at the base of the tower where the Overlord was once perched. Lloyd returns to them, and finds his father shows up, but he is no longer evil.