Season 1 focuses on the Ninja (Kai, Jay, Cole and Zane) fighting to determine whose the green Ninja (a ninja who is destined to fight the evil Lord Garmadon). Sensei Wu is struggling to maintain and teach his Ninja students. On the other hand, Lloyd Montgomery Garmadon (the son of Lord Garmadon and Misako nephew of Master Wu descendant and grandson of the First Spinjitzu Master and descendant and great-grandson of Firstbourne and Omega) accidentally releases the serpentine army to attack the ninja. Pythor is the main villain of season 1 & his main goal is to get all the fangblades to free his master and mistress 'The Great Devourer', so he can get destroy Ninjago city. Pythor is consumed by the Devourer, and the Devourer is destroyed by evil Garmadon (who uses the golden weapons), & later on steals the Golden Weapons. Also it was revealed that Lloyd (whose life was saved by Kai, due to his true potential) is the green ninja. And everything goes out of hand when a son has to fight his father.
Season 2 focuses on the Ninja trying to train Lloyd for the ultimate battle. On the other hand, Lord Garmadon uses the Mega Weapon ( a combination of the four golden weapons) for evil purposes. The Ninja are turned into children but are turned back to normal at the price of Lloyd losing his youth and becomes older. Lord Garmadon releases the Stone Army, due to the command of the OverLord. The ultimate battle begins, but Lloyd loses. On the second round the OverLord possesses Garmadon, claiming that Ninjago was never Garmadon's but he's. Lloyd becomes the Ultimate Spinjitzu master and defeats the OverLord, restoring Ninjago back to its good, original form, and destroying all Garmadon's evil, : turning him back to normal.
Season 3 focuses on the Ninja leaving in "New Ninjago City" (an update of original Ninjago city, a metropolis with multiple skyscrapers and advanced technology) and striving for action. At the time the Ninja find out that the OverLord is alive, & rebuilt himself into the Digiverse. The Ninja are given the Technoblades by 'Borg' (the creator of Borg Industries and the designer for New Ninjago City) which is the weakness for the OverLord. The OverLord infects every Android machine and robot with evil, including his Nindroid army. On the other hand, Jay is angry and jealous when it is revealed that Cole is Nya's love match, & for the entire season Jay and Cole fight. On the other hand, Garmadon is training Lloyd, at the point where Pythor is back and captures Lloyd for the OverLord to suck all his golden power so he can become the physical. When Lloyd is free he only has 10% of his golden power, which is divided to give the Ninja their elemental powers. The OverLord with his helper Pythor and launch Codename: Arcturus (the plan for them to get the golden weapons from space to make the OverLord become the Golden Master). The Nindroids go to space to get the Golden Weapons, but are privately followed by the Ninja. When they land on the asteroid, the nindroids get the Golden Weapons and fly back to Earth leaving the Ninja with a destroyed rocket ship. The Ninja use their powers to rebuild the rocket and fly back to Earth. The OverLord becomes the Golden Master, but is finally destroyed by Zane (who risks his life). And they have a sad memorial of Zane's bravery
On season 4 the Ninja are split due to Zane's sacrifice, But are reunited by Lloyd. The ninja participate in "The Tournament of Elements" hosted by Master Chen when they get the news that Zane is alive. They participate in the tournament with 12 other masters Skylor Chen (the Orange Ninja Wizard Sorceress Mage Magician and Master/Mistress of Amber and Absorption), Griffin Turner (Wizard Sorcerer Mage Magician and Master of Speed), Paleman also known as Mr. Pale (Wizard Sorcerer Mage Magician and Master of Light), Chamille (Wizard Sorceress Mage Magician and Master/Mistress of Form), Ash (Wizard Sorcerer Mage Magician and Master of Smoke), Bolobo (Wizard Sorcerer Mage Magician and Master of Nature and Plants), Gravis (Wizard Sorcerer Mage Magician and Master of Gravity), Neuro (Wizard Sorcerer Mage Magician and Master of Mind), Tox (Wizard Sorceress Mage Magician and Master/Mistress of Poison Toxic Acid and Venom), Shade also known as Shadow (Wizard Sorcerer Mage Magician and Master of Shadow), Karlof (Wizard Sorcerer Mage and Magician Master of Metal) & Jacob Pevsner (Wizard Sorcerer Mage and Magician Master of Sound and Music). In the Tournament Kai falls in love with Skylor Chen, & becomes Karlof's enemy (as they fight constantly in Episode 36 & 37). After many battles all the masters start to realize that when someone loses Chen uses his staff of elements to suck their powers for a transformation spell, which is performed by Clouse (Chen's number 2, Master of Dark Magic Dark Arts and a Wizard Sorcerer Mage and Magician). The spell makes everybody with the Andacondrai mark become Fake Andacondrai. The Andacondrai mark spot people include Chen himself, Clouse, Garmadon (who was revealed to be Chen's student), Skylor Chen (who was revealed to be Chen's daughter and spy), & every other Andacondrai wannabes. The transformation was not complete, and to complete it they'll need the saliva of a true Andacondrai (which was tiny Pythor in jail). When they took Pythor and complete the transformation, on the other hand, every elemental master has discovered all their elemental dragons. They fight all the Andacondrai wannabes. And the Andacondrai wannabes are sucked into the cursed realm, which leads to Garmadon sacrificing himself to be sucked into the cursed realm so he can unleash the Andacondrai spirits to curse Chen's army. At the end of season 4 Morro (Wizard Sorcerer Mage and Magician Master of Wind and Air and Sensei Wu's First Student and Pupil) is accidentally freed from the Cursed Realm.
Season 5 focuses on the Ninja fighting the ghost Morro (the Wizard Sorcerer Mage Magician and Master of Wind and Air and Sensei Wu's First Student and Pupil), Morro possesses Lloyd for most of the season. When Morro possesses Lloyd, the ninja lose their powers (for more than 3.5 quarters of the season) and use Aeroblades for most of the season. Morro unleashes a variety of ghost warriors (ghosts) & his mission is to find the realm crystal (a realm that can let its user travel through the 16 realms), & free his mistress, " The Preeminent" (the physical body of the cursed realm) so she can curse all 16 realms exept Djinjago. On the other hand, Nya is revealed to be the Water Waves Ocean Tides Fluids Ninja, as she is being trained by Sensei Wu. The Ninja and Morro struggle as they go through journeys to master Airjitzu (a Spinjitzu that can fly) to get the Sword of Sanctuary (a sword that can show the user the opponent's next move), and find the Realm Crystal. At the end of Season 5, Lloyd is free and fights with Morro, at the end Nya unlocks her true potential and destroys the Preeminent, with the cost of Morro dying. (note: the weakness of a ghost is water or deep stone [the aeroblades] ).
Season 6 focuses on the Ninja being famous, but is disrupted when Clouse (as a ghost) frees Nadakhan the Djinn (a djinn that grants you three wishes but on the third one, he captures you in the Djinn Blade/Sword of Souls). The whole season focuses on the ninja (mainly Jay) fighting Nadakhan's Sky Pirates Crew. Nadakhan's mission is to be married to Nya (because Nya looks like Delara:Nadakhan's love) so he can get infinite wishes. All the Ninja are captured but except for Jay/Nya. Nadakhan gets Infinite wishes but is stopped when Jay wishes that "nobody ever found the teapot and that Nya took his hand". This destroys the timeline of Nadakhan being free & reunites Jay and Nya's relationship.