Following their victory over Chen, the ninja face a new problem in the form of Master Wu's former pupil Morro who has escaped from the Cursed Realm and possessed Lloyd. During this, a shocked Nya learns that her mother was the previous elemental master of Water and she has inherited her powers. Nya then trains in order to master her abilities and after serious training she unlocks her true potential and destroys The Preeminent with this act, Nya becomes an official ninja.
Nya helped Wu open a tea shop known as Steep Wisdom following his retirement from being a master. Unfortunately business was short lived as on opening day, Morro attacked the shop seeking Wu's staff. Nya helped fight him off, but was ordered by Wu to flee in the Bounty with the Ninja.
Morro soon caught up with them and Nya donned her Samurai X gear to stop him. Nevertheless, the ghost crippled the ship and sent it crashing into a nearby forest. After Misako deciphered the message on Wu's staff, the Ninja departed for Stiix while Nya returned to Steep Wisdom with Misako and Wu. When they tried to explain the real reason why she was left back, which involved her parents, Nya revealed that Kai told her what Chen told him, looked into it and confirmed their father was the previous Master of Fire though Misako revealed their mother was the previous Elemental Master of Water. Much to her surprise, Wu revealed that the reason she was not allowed to join the Ninja was that she was in fact the next Elemental Master of Water--a revelation which shocked her into fainting.
Wu soon began Nya's training to become the Water Ninja, though she insisted she could aid the Ninja just as well being a samurai. Wu pointed out that a samurai was unable to perform Spinjitzu or summon an Elemental Dragon, and he summoned his own as an example. Master Wu said they would continue training until they find her weakness, for in weakness their is strength, to which Nya replies that it will be hard since she's good at everything she does. He presented her with the bucket challenge, wherein she had to fill a bucket with a hole in it completely full of water. This proved difficult for Nya and after trying all day, she gave up and tossed the bucket into the pond, not realizing that she had fulfilled her task by doing so. Wu tells Misako that he's found Nya's weakness, feeling weak. She's good at so much that when she comes across something she can't get master quickly then she doesn't even try.
While training with Wu, Misako revealed to him and Nya that Ronin was in the shop where he explained that Kai gave him the ninja's shares of the tea farm as payment for his shop being destroyed. He also revealed Morro had gotten the Scroll of Airjitzu and the Ninja were headed to Yang's Haunted Temple to receive another scroll.
While training, Nya was approached by Ronin and asked him to sneak her out so she could aid the ninja. At first, he refused not wanting to turn on Wu, but he changed his mind and agreed to take her at night after she bribed him. On the way to the Samurai X Cave, Nya saw Ronin put the money she gave him in a full safe in the back of R.E.X. and discovered the reason he had so much money was because he was trying to pay off a debt to Soul Archer. Upon coming in close proximity of the cave, they discovered that Morro was there trying to takes the mechs. Ronin tried to get Nya to leave since Soul Archer was there, but she refused, got in her mech and fought only to realize she couldn't even touch them with her weapons, though she did manage to destroy the Allied Armor of Azure before Morro could bring out reinforcements. Upon ejecting, she was horrified to see Ghoultar transform her mech into a ghastly, four-armed version of itself. She refused to leave, resulting in Ronin carrying her out which ended up with the ghosts surrounding them. Just as they were about to be captured, it began to rain resulting in the Ghosts retreating. Ronin was amazed it was raining in the middle of the dry season, to which Nya tried to pass off as luck, though Ronin told her she is meant to be the Water Ninja. After that, Nya gave up being Samurai X.
Now donning a Red and Light Blue Deepstone ninja suit, Nya accompanied the ninja, Wu, Misako and Ronin to the Wailing Alps. Prior to arrival, she comforted Cole on his becoming a ghost and to try to find what he can do now. After the Ninja were deployed, she monitored them from the Bounty control room up to until they crossed over to Cloud Kingdom through the Blind Man's Eye.
Ghoultar was brought aboard the Bounty and Nya questioned the ghost along with Wu and Ronin. However, when the ghost refused to answer, Wu decided that the time would be better spent training Nya and the two left, leaving Ronin in charge of the prisoner.
The two later returned and tried to bribe the ghost with food, though they were interrupted by the return of the Ninja who were in hot pursuit of Morro. As the Bounty took off to join the action, Nya mounted one of the cannons but was forced to fend off Ghoultar whom had escaped his prison. The Ninja were eventually brought on board with sword in hand and they left the mountain to search for the tomb.
Nya continues her training by trying to reverse the flow of the fountain only to fail. Exasperated, she complains as Ronin appears and tells her not to try too hard.
Later on, she appears in a part of the tea shop when Ronin shows up looking for the sword of sanctuary only to find it empty. Nya makes her presence known to Ronin showing him that she has the sword and states his earlier words made her think so she anticipated his plan. The two get into a fight with Ronin saying he wants the Sword and didn't want to hurt her as Nya states she was thinking the same. She soon looks at the sword and sees a future with Ronin kissing her and kicks him for it as he questions the reason to which she states "You know what you were about to do!" In her distraction, Ronin knocks her down and steals the sword just as Nya alerts her friends of his treachery. As they attempt to stop him the traps they made are triggered and incapacitate them allowing Ronin to escape.
Nya pursues thief who tricked her friends by having them pursue his empty ship and escaping in a boat. Nya tries to halt the river but it is too much and Ronin escapes while mocking Nya for trying to hard.
Nya remained aboard the Bounty with Misako and Wu while the Ninja pursued Morro into the Tomb of the First Spinjitzu Master. They ended up battling Soul Archer and Bansha, with Nya employing her elemental power by employing Ronin's advice and not getting overly worried about it. Unbeknownst to her, while the Ninja were in the tomb, all of them but Cole caught glimpses of the possible future, and Jay's saw him and Nya end up together. They were later relieved to see the Ninja emerge from the tomb, thought unfortunately the Realm Crystal was lost to Morro.
Nya and the Ninja returned to Steep Wisdom and discovered that Wu had sold the tea shop in exchange for some new vehicles from Cyrus Borg. Realizing that Morro had already seen the Ninja in action and knew what to expect, Kai suggested Nya take charge. She reluctantly agreed and explained her plan to the Ninja on route to Stiix.
After the Ninja determined the Realm Crystal was in Ronin's pawn shop, Nya dawned the Green Ninja gi and infiltrated the town, but was quickly caught. She was brought before Morro and she used her water abilities to destroy the ghosts surrounding the realm crystal so that Lloyd could get through and destroyed it. Unfortunately, they were too late and the Preeminent began to emerge.
As the Preeminent entered their realm, Nya and the other Ninja did everything in their power to stop it and its ghostly minions from cursing their home. Even her growing power, however, could only do so much; their best moves only slowed their adversary's progress to attack Stiix's villagers, which became worse when the ghosts armored their master with the village buildings so it could venture out to sea. Nya then jetted herself to the ferry to help protect the people.
When the incarnated Cursed Realm disabled the ferry from heading to deeper water, Nya contemplated all of the failures that occurred from the past day alone, leading to remembering her own from her life. Recalling Wu's advice to "not be afraid to fail", she realizes her fear of the unknown and unwillingness to learn from her mistakes were what held her back. Once she embraces and conquers this, she immediately turns into a whirlpool of aquatic energy and forms a titanic tidal wave which flushes all of the Preeminent into the deep sea and pushes the ferry from harm's way. Afterwards, she is more content and confident in her role as a ninja, having learned to just "go with the flow" of life.
Playing video games with the other Ninja, Nya is briefly lectured for not working with the others, but nevertheless shrugs off the advice. As the Ninja went off to help Lloyd at the hospital, Nya received an incomplete distress call from Ed and Edna, and arriving at their junkyard, witnessed several Nindroids surrounding the two atop a pile of junk. Destroying the machines, Nya was informed by an impressed, albeit dismayed Ed that the machines had merely been trying to help them down from the junk pile, having to be reprogrammed with vocabulary beyond the word 'Terminate'. Sheepish, Nya asked the two not to mention the incident.
Later, while helping Lloyd with his training to become a master, Nya, getting a phone call from Dareth, learned that Kruncha and Nuckal were causing chaos at the studios, enraged over not being cast as leads in an unofficial Ninja documentary. Not wanting to bother the others, Nya went down there herself, only for the two Skulkin to steal the D.B. Express' flyer, going off on it. Chasing after the two, Nya succeeded in defeating them, with an ecstatic Dareth noting the chase would be a hit; however, to her dismay, her chase had caused much damage.
Arriving back on the Bounty, Nya was comforted by Misako, who reminded her there was no shame in needing help, bringing Nya's spirits back up and causing her to heed her advice. However, upon hearing a report of Ghost Warriors attacking Stiix, Nya was forced to go on her own, asking an elderly couple to contact the Ninja to help her on the way, not knowing they had misheard her on her friends' location. Confronting the ghosts, who were vengeful over the Preeminent's death, Nya clashed with them, slowly being overwhelmed, only to be saved at the last minute by the others. Destroying the ghosts, the six of them celebrate, and afterwards helped host the Ninja For a Day Videogame Tournament at the hospital.