|“Whoa! How did Nya have time to build all this?”|
|— Lloyd to his father, regarding the Samurai X Cave|
The Samurai X Cave is an underground base built by Nya in a desert mountain. It serves as her personal headquarters and storage for her various machines, vehicles, and gear. During the Nindroid conflict, Garmadon and Lloyd entered the cave to get Nya's car, which they used in their effort to escape the Nindroids and prevent them from capturing Lloyd.
Following the defeat of the Golden Master, Wu and Nya began rebuilding Destiny's Bounty in the cave. When the Elemental Masters returned from Chen's Island, they met up at the cave to discuss their plan of action, as the second Serpentine War was about to commence. Some time later, Morro and several of his allies entered the cave to steal some of the gear there. Ronin and Nya tried to stop them, but Ghoultar corrupted Nya's Samurai Mech, transforming it into the Mech-enstein. Some time later, Wu assembled the Ninja at the cave to tell them Ronin and Misako went missing on the Dark Island.
After creating plans for the reconstruction of the Destiny's Bounty, Wu and Nya went to the Samurai Cave where they began rebuilding the ship. While they were working on it, Misako arrived reporting she had yet to receive word from Garmadon or the Ninja. Wu decides they must expand their search and Nya departs in the D.B. Express.
Misako attempted to use the cave's computer to contact Nya and Dareth but did not receive a response from either of them.
The Elemental Masters met up with Wu and Misako at the cave to discuss their plan of action, as Chen's army had arrived in Ninjago. The alliance formulated a plan to spread out and attack Chen's Noodle Trucks, which were transporting Chen's Anacondrai-turned followers.
Following the separation of the Elemental Masters, Lloyd had Neuro send a message to the other Masters, telling them to regroup in the cave. After doing so, they came up with the plan of stopping the Anacondrai Imposters in the Corridor of Elders.
Following Misako and Ronin disappearing on the Dark Island, Wu summoned the Ninja to the Samurai X Cave where he explained to them the situation.