Well, if Naruto is betrayed by Koneko in fanfiction, it could lead to a dark turn in Naruto's character. He might become more distrustful and cynical. Maybe he would start to question all his previous relationships and alliances. He could also go on a journey to find out the reason behind the betrayal and in the process, discover some dark secrets about the world he lives in.
One possibility is that Naruto becomes more isolated. After being betrayed by Akeno, he might find it hard to trust others. He could go off on his own to train harder and become stronger, vowing to never let such a betrayal happen again. This could lead to him unlocking new powers or abilities as he focuses solely on self - improvement.
One possibility is that Naruto's skills would be put to extreme use in ANBU's more secretive and dangerous missions. His unique abilities like the Shadow Clone Jutsu could be utilized in stealth and assassination operations, but he might also face a moral dilemma as ANBU often deals with morally grey areas.
One possibility is that Naruto could turn to the dark side. After being betrayed by his friends, his faith in the bonds he once cherished is shattered. He might start using his godlike powers for revenge, targeting those who wronged him. This could lead to a series of battles and a whole new dynamic in the Naruto universe.
He would be heartbroken. Naruto has a big heart and has always trusted his friends. This betrayal would be a huge shock to him.
Perhaps Naruto would try to find allies among the outcasts in the Highschool DxD world. Since he has been betrayed, he would understand the feeling of being alone and might reach out to those who are also on the fringes of society. He could form a new group that challenges the existing power structures in the Highschool DxD universe, using his unique abilities and his unwavering will from the Naruto world.
Latias could initially go into hiding, feeling hurt and betrayed. She might avoid Ash at all costs. Then, Ash could realize his mistake and start searching for her to apologize.
In this kind of fanfiction, Naruto might face a lot of challenges. Maybe Rias, for some reason, turns against Naruto. Naruto could find himself isolated and having to fight against Rias' forces. He would probably rely on his ninja skills and his strong will to survive.
Another possibility is a misunderstanding. Maybe some false information is spread about Naruto that makes Tsunade believe he has gone bad. In the world of Naruto, there are often enemies who try to create chaos by sowing seeds of distrust. Tsunade, without fully investigating, could fall for such a trick and seem to betray Naruto.
In such a fanfiction, it could be due to a misunderstanding. Maybe Naruto was forced into a situation where he had to act against the Yugioh world for the sake of his own village. For example, if there was a threat to Konoha that was somehow related to the Yugioh realm and he was given no other choice but to 'betray' them.
In such a fanfiction, Naruto might be betrayed by his new allies in the DxD world due to misunderstandings. For example, his powerful jutsu could be misconstrued as a threat. His loyalty to his own ninja way might clash with the values of the DxD characters, leading to a rift.