One possible scenario could be that Naruto's girlfriend betrays him because she is jealous of his godlike powers. Maybe she feels overshadowed and in a moment of weakness, she aligns herself with Naruto's enemies. It could lead to a great internal conflict for Naruto, having to face not only external threats but also the pain of betrayal from someone he loved.
The ending of Girlfriend Girlfriend manga is quite complex and bittersweet. The characters go through various challenges and their relationships evolve in unexpected ways.
One idea could be that the girlfriend, perhaps under the influence of an enemy, reveals Naruto's bloodline secrets to those who would use it against him. For example, she might be tricked into thinking she's helping Naruto in some way, but actually endangering him.