Fanfiction writers sometimes justify it by introducing new elements to the Naruto world. They might create new types of chakra or energy sources that Naruto can tap into. For example, there could be a 'divine chakra' that only Naruto can access due to his special heritage. Or they might say that Naruto's bond with his friends and the village is so strong that it manifests as these impossible powers. His desire to protect everyone and his love for his friends and home somehow unlocks these powers that are beyond the normal scope of the Naruto universe.
Well, often they use the idea of Naruto's strong will. They say that his will is so strong that it breaks the normal limits of what is possible in the Naruto universe. So, his will allows him to access these impossible powers. Also, in some fanfictions, Naruto goes through some extreme and unique training or experiences that no one else has had, and this is what gives him these extraordinary abilities. For example, he might travel to a different dimension where the laws of physics and chakra are different, and when he comes back, he has these new powers.
Some writers justify it by saying that Harry is a descendant of a powerful ancient magical line that was long forgotten. This hidden heritage unlocks his godlike powers as he grows older and discovers more about his past. For example, he might find out that his ancestors made a pact with some powerful magical beings, and the powers are now passed down to him.
In some fanfictions, Naruto might have the power to control time. For example, he could freeze time during battles to gain an advantage. Another impossible power could be the ability to instantly teleport to any location in the ninja world without using any known jutsu. He might also have the power to communicate with all living beings telepathically, which is not part of his original abilities in the official story.
Some writers justify it by creating a situation where Sasuke has to make a great sacrifice. For example, he might give his life to protect Naruto or the Hidden Leaf Village from an overwhelming threat. His selfless act in these scenarios is seen as a way to atone for his past mistakes and show his growth as a character.
Another way is through a series of tragic events. If Naruto experiences multiple losses, such as the death of his closest friends or mentors, he could become disillusioned with the world. Writers can show how this grief and anger transform him into a corrupted version of himself, as he starts to question the values he once held dear.
Fanfiction writers could use power imbalances. If Naruto has suddenly gained a lot of power and doesn't fully control it, he could accidentally hurt Sasuke. It shows the consequences of power and the need for control in their relationship.
They could also use the idea of being influenced by dark powers. Maybe Naruto comes into contact with a powerful and malevolent force that slowly corrupts him, making him do things that are out of character for the original Naruto. This gives the writer a way to explore a different side of the character while still having a somewhat believable reason for his actions.
They might justify it through misunderstandings. Maybe Arthur is tricked into a situation that looks like cheating but he's really trying to protect Merlin in some convoluted way.
They might justify it through her past traumas. For instance, if Sakura has faced repeated rejections or has been constantly overshadowed in the original story, a writer could use this as a reason for her to betray. She could feel that she has been treated unfairly and that her so - called friends never really understood her pain. So, in the fanfiction, she decides to take a different path that is seen as a betrayal to those around her.
Some writers might justify it by exploring the idea of redemption. They could write Voldemort in a way that shows a glimmer of humanity that Harry, being abused, might be able to relate to on some level. Maybe Voldemort has a hidden past that makes him more complex than just the evil wizard we know.
A possible justification could be a deep exploration of Harry's post - traumatic stress. Writers might think that after years of fighting and losing so many people, Harry could reach a breaking point. But really, the Harry Potter we know from the books has a strong will and a support system that should prevent such a tragic end. So, these justifications seem more like attempts to create shock value rather than staying true to the character's nature.