Nya and her friends come to the aid of Master Wu when he battles a villain who can control time with a mysterious gauntlet. Later said man and his brother lead an army of new serpentine warriors with armor Kai recognizes and tells Nya their parents possibly made it leading him to investigate. While he does that, Nya learns someone has taken her old Samurai X armor leading her to take on her own investigation and finds out this mysterious person has taken up the mantle for themselves. Later on, she and her brother are reunited with their parents and learn some disturbing details of their past. The two are later forced to help the Time Twins when they threaten their parents
Nya was jealous that someone stole her old armor and wanted to best the new Samurai X. She later returned to the Samurai X Cave where she found the mysterious new samurai.
Nya returned to the Samurai X Cave where she found the new Samurai still lurking. Still angered about the theft of her suit, Nya attacked the warrior and the two engaged in a battle throughout the cave. However, the mysterious figure used a voice scrambler and as their fight continued, it attempted to assume the identity of multiple people including Ronin, Dareth, Misako, and even Garmadon. However, it was only when the new samurai took on Nya's own voice in an attempt to convince her of the importance of keeping its identity a secret. Realizing it was time to pass the mantle onto a worthy successor, Nya yielded. She presented the Samurai VXL to the new warrior, but was then summoned to Chen's Noodle House by Kai.
Upon arriving at the Noodle House however, Nya was horrified to find Skylor present, thereby ruling her out as the possible new samurai. As she took a seat, Kai revealed to Nya that he had found an old Vermillion helmet back at Four Weapons, thereby proving that their parents worked for the Hands of Time. Before they could talk further however, Nya received a call from Lloyd informing her that the other Ninja had found the lair of the Hands of Time. As she and Kai set off towards the coordinates, Nya realized that this meant they were also heading to where their parents were.