The Serpentine War was a conflict that took place thousands of years after the first defeat of The Overlord and his Stone Army by the First Spinjitzu Master, and several decades before the era of the ninja began. It was fought between the five tribes of the Serpentine and the people of Ninjago, with the Anacondrai and the Elemental Masters serving as leaders of the respective sides.
The Serpentine were wreaking havoc on Ninjago, raiding places like Jamanakai Village and terrorizing those living there. The Elemental Masters formed an alliance to battle the Serpentine and protect the citizens. At Jamanakai Village, the Elemental Masters drove back the Serpentine Tribes, but were forced to retreat upon the arrival of the Anacondrai. A crucial battle in the war took place at Birchwood Forest, with the Elemental Alliance fighting Arcturus and his Anacondrai, but this battle was lost as well. The Elemental Masters found hope by using the Sacred Flutes to hypnotize the Serpentine and imprison them in a series of tombs. Arcturus and the other Anacondrai generals were found guilty of committing war crimes, and were consequently banished to the Cursed Realm.
Lloyd Garmadon, in his bid to force the people of Ninjago to respect him as the successor to his father Lord Garmadon, threatened to unleash the Serpentine upon them. The Ninja noted that the Serpentine had long ago been sealed away in ancient tombs.
Seeking answers regarding the Stranger helping the Digital Overlord, the Ninja visited the Serpentine in their new home beneath New Ninjago City. There, they were told the legend of the Golden Master, a monstrous being whose coming had been foreseen by the Serpentine. Seeking to avert this crisis, the Serpentine tried to warn the humans, but were perceived as attacking them and driven underground.
While searching for Nya, Garmadon related to Lloyd his history with Master Chen during the Serpentine War. The conflict was a desperate one, made more so by the presence of the Anacondrai under Arcturus. Eventually, under the leadership of Wu and Garmadon, the Elemental Masters formed an alliance that saw some victory against the Serpentine - however, Chen managed to turn some of the masters against the others. Fortunately, they found their trump card in the Sacred Flutes, which they used to halt the Serpentine and drive most of them into their underground tombs. Arcturus and the other Anacondrai generals were then magically banished to the Cursed Realm. In the meantime, Chen and his disciple Clouse who sided with the Anacondrai 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
However, upon finding Nya, the latter showed Lloyd the spell as Garmadon realized that Chen intended to renew the war by transforming himself and his warriors into Anacondrai. Soon enough, a Second Serpentine War would commence, with the Elemental Masters fighting against Chen and his army of fake Anacondrai.
- There is a rather large plot hole in the story of the Serpentine Wars. In the first season of the series, it is explained that the five tribes of Serpentine all fought against each other for rule over Ninjago. In the 2014 episode "The Curse of the Golden Master", Acidicus explains that all five of the tribes tried to warn the people of Ninjago about the coming of the Golden Master, but they thought the Serpentine were the enemy and that started the wars. Then, in a flashback from the 2015 episode "Spellbound", all five of the tribes are seen working together against the Elemental Alliance, later revealed to have been tricked by Chen into fighting them. The concept of the five tribes battling against each other is ignored at least twice in these later explanations of the wars. Also, the Elemental Alliance was never mentioned as being involved in the Serpentine Wars prior to the flashback in Spellbound.