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The Sacred Flutes were legendary instruments in Ninjago, appearing as traditional wooden flutes. It is said to have power over the Serpentine, being capable of weakening them and negating some of their abilities.
The Sacred Flutes were originally conceived by Garmadon as he watched a flute player hypnotize a snake. Multiple flutes were made and distributed among the Elemental Masters, who used them to defeat the Serpentine and lock them away in tombs.
By the time that the Serpentine were released by Lloyd, Master Wu had the only remaining Sacred Flute. He used it to cure Cole of Skales' Hypnobrai Hypnotism while the brainwashed ninja fought his comrades atop Lloyd's Treehouse Fortress. Upon hearing the music of the flute, Cole immediately snapped out of his trance and joined his allies in escaping the crumbling fortress. On the way back to the Monastery, Wu explained the flute's significance to his pupils.
Master Wu brought the Sacred Flute with him when the Ninja visited Ed & Edna's Scrap N Junk. It proved useful in stunning the Fangpyre forces occupying the junkyard, but Lloyd countered its effects by using a boom box infected with Fangpyre venom, playing loud music to drown out the sound of the flute.
When Cole and Zane investigated the Constrictai Tomb, they took the Sacred Flute with them. During their battle with Constrictai General Skalidor, they repeatedly attempted to use the flute, but Skalidor's powerful grip left them unable to finish the song. After several tries, Zane finally completed the melody, weakening Skalidor enough for the two Ninja to defeat him.
Later, the Ninja were lured into a trap in the Toxic Bogs, where they learned that all of the Serpentine had been unleashed. When Zane attempted to use the Sacred Flute against the massed Constrictai and Venomari, Pythor knocked the flute out of his hands and took it for himself. Master Wu was displeased to learn that the Serpentine now possessed the flute.
Pythor would eventually use the Sacred Flute against his fellow Generals in a bid to unite the tribes under his leadership. After letting Skales in on his plan, he challenged the Generals to a Slither Pit in The Lost City of Ouroboros, demanding their allegiance if he managed to defeat all four of them at once. When the battle turned against Pythor, Skales slipped him the Sacred Flute, and the scheming Anacondrai used it to incapacitate the other Generals. Both Pythor and Skales had put cotton balls in their ears prior to the battle, so they were not affected.
This was the last time the actual Sacred Flute was seen. It was presumably destroyed by the Serpentine to prevent it from being used against them.
Zane was revealed to have a recording of the Sacred Flute, which the Ninja used in the construction of the Ultra Sonic Raider. The vehicle's main armament was a pair of sonic cannons that played the Sacred Flute's melody at an amplified volume, which the Ninja used against The Great Devourer. The monstrous snake proved as vulnerable to the music as the Serpentine had, but it managed to disable the Raider's sonic cannons with its tail before the Ninja could completely pacify it.