Following the loss of Zane, the Ninja were pulled into the Tournament of Elements, with the hope of reuniting with Zane. The Ninja found themselves competing with the Elemental Masters of their generation in a series of events. Chen tried stealing the Elemental Masters' powers to transform him and his army into Anacondrai, but when his Staff of Elements was destroyed, he had to use his own daughter and the last living Anacondrai to complete the spell. Chen's army of fake Anacondrai attacked Ninjago and its people, commencing a second conflict between man and snake.
The fake Anacondrai eventually faced off against the Elemental Masters at the Corridor of Elders, which was the most crucial location of the conflict. Chen's army was overwhelming the Elemental Masters and their allies until Garmadon sacrificed himself to free the spirits of the Anacondrai generals from the Cursed Realm. The generals condemned Chen and his army to the realm, with the Elemental Masters emerging victorious in the conflict.
Chen designed the Tournament of Elements which brought together the current generation of Elemental Masters, some of whom’s powers he hoped to steal and absorb in the Staff of Elements so that he could fulfill a transformation spell and transform him and his followers into Anacondrai.
Chen began the tournament by having the Elemental Masters fight over Jadeblades. Whoever didn't have one would be eliminated. The first Elemental Master to lose was Karlof, who Chen had fall through a trapdoor.
The remaining Elemental Masters are taken on blimp being told to hunt down Nya who stole the spell Chen required. He tells them he left items to help them capture her before letting them off the blimp.
After landing, Garmadon tells Lloyd the story of his past with Chen and the previous first Serpentine War. During his time with Chen, he was given the title of Lord by him and wrote his name on a love letter written by his brother to Misako. When war broke out between the Serpentine and Elemental Masters, Chen sided with the Serpentine while Garmadon defected to join his brother and to see Misako.
The war was fierce but Garmadon found a solution that gained victory. By having the Elemental Masters hypnotize the Serpentine using Sacred Flutes, they were able to imprison the five tribes in a series of tombs. Arcturus and the Anacondrai generals were put on trial and found guilty of war crimes. Consequently, the seven generals were banished to the Cursed Realm. In the meantime, Chen and Clouse were exiled to a secluded island for siding with the Serpentine.
Afterwards, Chen informed Clouse the items he gave the masters were implanted with tracking devices. He then had Clouse and the other Anacondrai Cultists round up the remaining Elemental Masters.
One by one each master was captured and placed in cages made of Vengestone. Only two avoided this fate, Skylor, Chen's daughter and spy, and Lloyd, who didn't take any of Chen's items.
Chen's plot was revealed to Lloyd by Nya, who had previously broke into Chen's Palace, as Garmadon realized Chen's goal was to transform him and his followers into Anacondrai, which would begin a new war.
That night, in the Anacondrai Temple, Chen stole the elements of the masters he had captured and imprisoned them. Then, at the behest of Skylor, he released Kai. Chen tempted him to turn against Lloyd by offering secret information about his parents. It appeared that Chen "succeeded" in turning Kai, as the latter would aid him in drawing Lloyd out and getting him to face off against Chen. Lloyd and Chen engaged in fierce but short battle as Chen used the stolen elements of the other fighters to overwhelm Lloyd and defeat him.
When Chen defeated Lloyd, he stole his element, before taking the element of his daughter, Skylor. With all elements gathered, Chen prepared to use the spell to transform into Anacondrai however, Kai and Skylor revealed their true colors by disrupting the spell and taking away the staff. The others Elemental Masters then broke in and fought back against the Cultists, as Kai destroyed Chen's staff allowing everyone to reclaim their elements. With their powers restored, they defeat the Cultists forcing Chen and a select few of his followers to escape while taking Skylor as their hostage.
The Elemental Masters take over Chen's Island, trapping the Anacondrai Cultists while in the meantime, unbeknownst to them, Chen, Kapau and Chope were fulfilling the transformation spell using Skylor's element. Eventually, the spell was completed, turning Chen and his entire army into Anacondrai. The Elemental Masters tried fighting back, but the fake Anacondrai proved too strong. Eventually, the fake Anacondrai retreated, abandoning the stranded Elemental Masters on the island and heading off to terrorize Ninjago.
Fortunately, the Elemental Masters gained the resolve to unlock their own Elemental Dragons, using them to escape the island and pursue Chen's army.
The Elemental Masters reached the city a day after Chen only to find he hasn't yet invaded. Having their allies watch over the city, the Ninja reconvene at the Samurai X Cave which became their base of operations during the conflict. There, they devised their next plan of action.
Chen and his Cultists set up a camp in Ninjago's subway system. While there, Chen noticed the transformation was wearing off and the Cultists were becoming human again. In the Book of Spells, Chen found that the transformation could be made permanent through the essence of a true Anacondrai. As such, Kapau and Chope set off to Kryptarium Prison to capture the last surviving Anacondrai, Pythor.
The Ninja had journeyed to the prison as well for answers on how to fight Chen's forces prior to the cultist break in. A fight broke out between them, and as this happened Zane saw Pythor's venom fall onto Garmadon's recently turned human hand, transforming it back. Zane deduces the Cultists came for Pythor to maintain the transformation. Lloyd and his family take Pythor away from the battle since Chen needs him for his invasion plan. As they run, they discuss the Serpentine War and how Chen was talking about which side was going to attack first and Lloyd realizes Chen deceived both the Elemental Masters and Serpentine into fighting each other in order to benefit himself.
After fighting the Ninja, the Cultists were aided by other Cultists, who had captured Pythor and used his sweat to make the transformation permanent.
An army of what seemed like at least two-hundred fake Anacondrai spread out across Ninjago in Noodle Trucks, with the Elemental Masters setting off to stop them. However, upon stopping each of the trucks, they found they were all empty. With the Elemental Masters divided, Chen's army began attacking Ninjago, first with Jamanakai Village—a pivotal location in the first war. Realizing what is happening, Garmadon proclaims that the new Serpentine War has begun.
Chen's army continues spreading out across Ninjago, with the intention of conquering every village and not stopping until they do so. In the meantime, Lloyd has Neuro rally the Elemental Masters at the Samurai X Cave, with Neuro using his element to send the message. At the cave, Nya announced the Cultists have conquered Ninjago's eastern coast. Wu suggests staging a battle at the Corridor of Elders, which could end the war before it escalates. The Elemental Masters agree, and they head off into the city to rally support from the citizens, most notably the Serpentine.
Chen's army makes its way through the Corridor of Elders, though they don't expect the fight and were simply passing through the canyons. The Elemental Masters and their allies block off the Corridor to prevent Chen's army from passing through, with Lloyd using his element to create a line in the ground, which they cannot allow the Anacondrai to pass. Seeing the alliance far ahead, Chen orders his army to charge. The fake Anacondrai slither towards their adversaries, but their attack is cut short as the ground caves in before them. Zane seals the crevice with a blast of ice and the battle begins. At first, the Elemental Masters overwhelm the Anacondrai and they begin to retreat, but Chen forces them to continue the battle. The fake Anacondrai charge at the Ninja once more, this time attempting to cross the line that Lloyd drew. Chen takes off in the Roto Jet along with several Blade-Copters. One Blade-Copter is quickly hijacked by Shade, who uses it to fire down upon Chen's army. Despite this, the fake Anacondrai continue their attempts to cross the line, shoving back the Elemental Masters who give their all to hold their ground.
High above, Destiny's Bounty 2.0 joins the battle, shooting down at the Cultists and using its massive anchor to destroy several Condrai Crushers and Condrai Buggies. Angered by the appearance of the Bounty and growing impatient, Chen fires the Roto Jet's missile launchers at the Corridor's right wall, collapsing part of it. Gravis uses his element to prevent the falling rocks from harming anyone, but with the new opening in the canyon the fake Anacondrai cross the line and break pass the alliance. As this happens, Pythor arrives at the scene, riding a swamp rat and carrying the Book of Spells. Pythor meets up with Lloyd telling him to take him to his father as he knows of a way to defeat Chen's army. Unsure, Lloyd ponders on this as Pythor promises he won't try treachery as he'd prefer to take over himself. With that answered, Lloyd takes the Anacondrai aboard the Bounty, to find his way to end the conflict.
Aboard the ship, Pythor tells Wu and Garmadon of a spell that can allow for prisoners of the Cursed Realm to be released, but only if the one who cursed them takes their place. Pythor suggests they release the original Anacondrai generals, who would be infuriated by Chen's army of fake Anacondrai, but this would mean Garmadon must make the sacrifice and take their place. Garmadon comes to accept this, knowing they have no other choice, but Lloyd is infuriated that his father would walk out on them and leaves taking out his rage by furiously attacking Chen's army with all his might. On the Bounty, Wu begins reading the spell to banish Garmadon, who apologizes to his wife for lying to her but she states she had already forgave him. Garmadon tells her to apologize to their son for him but Lloyd returns and reads the rest of the spell himself. Garmadon stated he had always wanted to make the world into his image but sees he already did so through his son.
Once the spell is complete, Garmadon ascends to a portal in the sky, which he disappears in as the spirits of the Anacondrai generals emerge. The generals fly into the Corridor of Elders and begin cursing Chen's army, turning them into ghosts and carrying them into the portal. Chen is confronted personally by Arcturus, who he pleas to but is ignored as the latter denounces Chen as a liar, a cheat and impostor before condemning him to the Cursed Realm. With Chen's army banished, the portal closed, and the war came to an end. Afterwards, the Anacondrai generals thank Pythor, whom they restore to normal size, and Lloyd for releasing them so they can bring peace to Ninjago, calling the Ninja and their allies to forever fight in Ninjago before heading to the Departed Realm at peace.
Later on, the Elemental Masters make amends with the Ninja as they part ways but not before promising to offer future aid in other conflicts.
With the war over, statue of Garmadon is built in the monuments of the Corridor to pay respect to him. They then swore to defeat any future threats and make sure that Ninjago City remains safe from any villains.