Maybe the wings are related to a new form of chakra she discovers. As female Naruto experiments with different chakra natures, she accidentally unlocks this winged form. This form could have unique abilities like being able to fly at supersonic speeds or creating powerful wind-based attacks with the flaps of her wings. It could also lead to a storyline where other ninja clans become jealous or fearful of her new power and try to either steal it or get her to suppress it.
The wings could be a curse in disguise. At first, Naruto is excited about having wings, but she soon realizes that they attract dark spirits or are a sign of an impending doom for the village. She then has to embark on a journey to find a way to either control the wings' negative effects or get rid of them altogether. Along the way, she meets old friends and foes who either help or hinder her progress.