It could be that Skyla has a long - held secret ambition. When Ash unknowingly gets in the way of her achieving it, she feels betrayed by him. For example, if her ambition was to be the sole trainer of a certain rare Pokémon and Ash catches it first. This could lead to a complex and emotional story of betrayal and forgiveness.
Perhaps Ash is wrongly accused of something in Skyla's hometown. Skyla believes the false accusations and turns her back on Ash, which makes Ash feel extremely betrayed. He then has to prove his innocence not only to Skyla but also to the whole town.
One possible plot could be that Ash discovers Anabel has betrayed him by siding with a rival trainer in a crucial tournament. This could lead to a rift in their friendship and Ash having to find a way to overcome this setback and prove himself without her support.
One possible plot could be that Ash is falsely accused of a serious crime within the Pokémon world, and Greninja, due to some misinformation or outside influence, turns against him. Maybe a powerful villain manipulates Greninja's mind, making it believe that Ash is a threat to the Pokémon world. This could lead to intense battles between them, with Ash being heartbroken and trying to prove his innocence while also trying to save Greninja from the villain's control.
Perhaps a new and powerful trainer arrives in the story. This trainer manages to deceive Ash's harem members, making them think that Ash is a hindrance to their growth as trainers. As a result, they side with the new trainer and betray Ash, leaving him feeling confused and alone.
It could be a new character who is jealous of Ash and Skyla's friendship. This character might spread false rumors about Ash to Skyla, causing her to feel betrayed. So, this new jealous character would be the main antagonist.
Perhaps the aura guardian was mind - controlled. An evil force took over its mind and made it act against Ash. In this case, the story could revolve around Ash trying to break the mind - control and save his friend. It would involve a lot of action and mystery as Ash figures out what's wrong and how to fix it.
It could be that Arceus betrays Ash by revealing that all of Ash's Pokemon encounters and relationships were fabricated. Arceus made it so that Ash would form bonds with certain Pokemon to further its own ends. For instance, Arceus wanted to study the power of friendship among humans and Pokemon through Ash's experiences. When Ash finds out, he feels used and betrayed. He might then set out on a journey to free his Pokemon from Arceus' control and restore their true free will.
One common plot could be that Ash is betrayed by a so - called friend in the Pokémon world who teams up with a rival trainer to undermine his journey. Maybe this friend spreads false rumors about Ash's training methods. Another plot might involve Dawn being betrayed by a coordinator she trusted. This person could steal her unique Pokémon training techniques and use them for their own gain. There could also be a plot where both Ash and Dawn are betrayed together by a powerful Pokémon organization that wants to stop their progress in the Pokémon world.
Well, perhaps in the fanfiction, Ash gets influenced by a powerful and devious trainer. This trainer makes Ash believe that May is holding him back in his Pokémon journey. So, Ash starts to distance himself from May, not realizing he's being manipulated. May, on the other hand, is left heartbroken and feeling betrayed as she doesn't understand why Ash is suddenly so cold towards her. It could also be that Ash enters a Pokémon tournament without May, even though they had promised to do it together all along.
One possible plot could be that Tails is betrayed by a close friend who becomes jealous of his intelligence and skills. For example, Sonic might start to feel overshadowed by Tails and in a moment of weakness, turn against him. This could lead to Tails having to fend for himself and prove his worth all over again.
He might be initially shocked. Ash has always been surrounded by friends and supporters, so suddenly being betrayed by everyone would be a huge blow. He could be in disbelief for a while.