Ambush at the Ancient Temple
After both Lilac and Carol rescued Torque from Serpentine, the girls embarked on a quest to prevent the Kingdom Stone from being stolen. They met Neera and General Gong at the Ancient Temple and tried to warn them that the Kingdom Stone was in danger of being stolen by the Soldiers of Shang Mu. She refused to heed their warning, which had resulted in Soldiers in disguise successfully ambushing them and taking the Kingdom Stone, with help from Spade.
After the girls returned from the negotiations with Mayor Zao to inform the Magister that the Kingdom Stone was now in the possession of Shuigang, it was shown that Neera conducted an investigation on Lilac and Carol, knowing their first and last names as well as their past connection to the Red Scarves. She presented her own theory, which states that the girls are not what they claim to be, and are sent by Zao to deceive the Magister. The girls were then imprisoned upon the Magister's order by her hands, while Torque was placed in quarantine.
Traitors to the Law
After the girls broke free from the prisons of Shang Tu, Neera and the Bird Officer initiated many attempts to put them under arrest and return them to prison, all of them ending in failure, including an attempt where she was accidentally frozen by an ice missile. In the end, she could only capture Lilac, who gave up easily due to her inability to fight or flee because at that time, she was severely injured from being brutally tortured at the Thermal Base, by Lord Brevon himself.
The Magister's Mission
Upon returning to Shang Tu, Neera brought the injured Lilac before the Magister, who confessed to being foolish for distrusting her and her friends, telling her that their evidence was examined, he then tasks her with an important mission. After Lilac was fully recovered in a medical sauna, Neera explains to her that the fragment Torque gave them earlier was indeed crafted from a rare mineral that was found in one other location, which was abandoned due to fear of radioactivity. Following that explanation, she sends Lilac to Pangu Lagoon. Later, Neera accompanies Lilac and Pangu to the Snowfields, to stop the armies of Shang Tu and Shang Mu from waging war on each other.
A New Beginning
At the end of the game, Neera tended to Milla, who was distraught for being mutated by Brevon and attacking her friends (in Milla's story, she tended to Carol). Later, she attended a royal dinner in Shang Mu with Mayor Zao along with the girls, Torque and Gong. Neera looked at the girls, smiling, knowing of the courage they've demonstrated in the recent battle that changed the future of their planet; and likely saw to it that they were pardoned for their past crimes.
Neera continues to serve as the Magister's adviser, and also works closely with Lilac, Carol & Milla. She helps them in their training and directs them to do missions for the Magister. She'll also aid them in battle with the use of her Frost Arts to capture criminals easily and non-lethally.