The Second Serpentine War was a conflict that took place following the Tournament of Elements and prior to the Battle of Stiix. It was fought between the Elemental Masters and Chen's army of fake Anacondrai. The conflict followed the Serpentine War, a battle fought decades prior by the current Elemental Masters' ancestors.
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 battle. 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.
In the first Serpentine War, Chen deceived the Elemental Masters and Serpentine into thinking each side was out to attack the other first, which prompted both sides to fight each other. The Elemental Masters managed to hypnotize the Serpentine using Sacred Flutes, and the five tribes were imprisoned 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 his disciple Clouse were exiled to a secluded island. Over the years, Chen built up his criminal empire there, worshiping the Anacondrai despite the fact that he tricked them during the Serpentine War.
Chen's Tournament of Elements brought together the next generation of Elemental Masters, whose 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. This plot was discovered by Nya when she broke into Chen's Palace.
Clouse and the other Anacondrai Cultists rounded up the remaining Elemental Masters after they jumped out of Chen's Blimp. That night, in the Anacondrai Temple, Chen stole their elements before meeting with Kai, whom he succeeded in turning against Lloyd and getting him to face off against Chen. When Chen defeated Lloyd, he stole his element, before taking the element of his daughter, Skylor. However, the Elemental Masters fought back against the cultists, destroying Chen's staff and reclaiming their elements. Chen retreated with his daughter, intending to use her element to complete the transformation spell instead.
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 Elemental Masters on the island and heading off to terrorize Ninjago. Fortunately, the Elemental Masters unlocked their own Elemental Dragons, using them to escape the island and pursue Chen's army.
The Elemental Masters met up 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. After fighting the Ninja, they were aided by the other cultists, who captured Pythor and used his sweat to make the transformation permanent.
An army of 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 are 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 cult 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 Bladecopters. One Bladecopter is hiijacked 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 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 through the alliance. As this happens, Pythor arrives at the scene, riding a swamp rat and carrying the Book of Spells. Lloyd takes Pythor aboard the Bounty, as Pythor promises he has a way to end the conflict and defeat Chen's army.
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 and in his rage attacks Chen's army with all his might. On the Bounty, Wu begins reading the spell to banish Garmadon, but Lloyd returns and reads it himself. 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 denounces Chen before condemning him to the Cursed Realm. With Chen's army banished, the portal closed, and the war came to an end.