Since Lord Garmadon's disappearance, Ninjago has been at peace; but when Garmadon's son releases the five ancient tribes of the Serpentine, the Ninja had to learn how to unlock their full potential to combat the growing threat.
The ninja's new mission is to train Lloyd and they find a place to begin the training. Meanwhile Lord Garmadon enslaves the serpentine into turning the wreckage of the Destiny Bounty into his new ship.
Lord Garmadon brings the pirates of Destiny Bounty back to life, but they take over the new Black Bounty and attack Ninjago City. While the ninja defend the city, Lloyd unlocks his spinjitzu power.
When our heroes are invited back to Darkly's Boarding School, they discover it's a trap set up by Lord Garmadon and his evil replica ninjas created by Garmadon's new Mega-Weapon.
When the ninja learn that Darreth's Mojo Dojo is to be destroyed and Darreth doesn't have the money to save it, our heroes enter the annual NinjaBall Run to win its cash prize in order to save the dojo.
When the Ninja interrupt Garmadon from using his Mega-Weapon to 'turn back the clock' and bring to life the fossils of a monster, the Ninja are hit and turned into kids and are now forced to enlist Lloyd's help to battle the awakened monster.
When Garmadon travels back in time in order to undo the past and rid the Ninja from the future, the Ninja follow him and try to stop him by using the Golden Weapons from the past to clash against Garmadon's Mega-Weapon.
The ninja face off with an exhibit of a Stone Samurai Warrior that the toxic venom from the Great Devourer has brought to life while Garmadon manages to find a fabled Dark Island that is said to hold dark powers.
The ninja try to flee from the rest of the Stone Army that has been brought to life by the Devourer's toxic venom - and things get a lot worse when Garmadon arrives with a 'Helmet of Darkness' and seizes control of the Stone Army.
The Ninjas, Lloyd, Sensei Wu and Misako journey to the Dark Island to find a 'Temple of Light' that can restore the Ninjas' elemental powers but are attacked by Starteeth (barnacle-like star fish) that start eating through their ship.
After battling off Garmadon's Stone Army, the Ninjas finally arrive at the Temple of Light where they harness their pure elemental powers, concentrating them onto Lloyd who becomes more powerful than he ever imagined.
When the Ninjas' attempt to return Garmadon's 'Helmet of Darkness' to its perch at the Celestial Clock in order to prevent the final battle between Lloyd and his father from beginning fails, a Super Weapon is created that can destroy all of Ninjago.
Garmadon's ultimate weapon, the Garmatron (Which in effect is a giant Cannon), is completed. The Overlord, the Stone Army, and Garmadon drive the vehicle to the coast of the Dark Island, but not before testing it out on Nya. The Ninja pursue Garmadon to the coast, and discover that Nya has turned evil, gaining all of Garmadon's dark abilities in the process. Kai, Jay, Zane, and Cole stay behind to deal with Nya, while Lloyd, Misako, and Sensei Wu rush to stop the Garmatron. They fail, and Garmadon turns Jamonkai Village, and the town around Four Weapons evil. The shift in the balance of good and evil allows the Overlord to poccess Garmadon's body and begin to transform into his original form. Lloyd challenges him, but is injured in the resulting battle. The Overlord attempts to turn Lloyd, Wu, and Misako evil with the Garmatron, however the Tinkerer appears in Destiny's Bounty, and crashes it into the missle before it hits them. The whole Stone Army and the Overlord create a portal to Ninjago City, and head there to turn the rest of Ninjago evil. With the Destiny's Bounty now destroyed, the Ninja have no way to get back accross the sea and stop them.
Time is running out for the ninjas as the Overlord have reached Ninjago city. However, the ninjas, Sensei Wu, Misako and the Tinkerer are still unable to return to Ninjago.