Just as the rebuilding effort in Ninjago begins, the four ninjas come to realize that evil has started to resurface with Lord Garmadon forging the ninjas' lost Golden Weapons into a Mega-Weapon with unspeakable powers.
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.
A great darkness has fallen upon Ninjago as Garmadon's Super-Weapon has turned it evil but Lloyd and the Ninjas discover that light is more powerful than dark - and the final and ultimate battle is on.