Well, perhaps in the fanfic, Cloud gets transported to a time when the Cetra were still a thriving race. He has to adapt to their way of life and in the process, learns their magic and philosophy. He then uses this knowledge to solve a great crisis that threatens both his world and the remnants of the Cetra world. He becomes a sort of bridge between the two cultures.
It could be a power - hungry human who fears Cloud's new Cetra powers. This person might see Cloud as a threat to his own plans of domination and tries to eliminate him before he can fully master his abilities.
Perhaps it turns out that Cloud's death was faked by an enemy in order to break Tifa's spirit. But Tifa, being strong - willed, sees through the ruse and uses the situation to her advantage to take revenge on the enemy.
One possible plot development could be Naruto's ideals getting warped due to some traumatic event. For example, if he fails to save a dear friend, he might start to believe that the only way to achieve true peace is through extreme force. Another development could be his relationships turning sour. Maybe his friends start to fear his new, twisted self and Naruto, feeling betrayed, becomes even more deviated from his original self. Also, his view of the ninja world could change completely, seeing it as a place that needs to be remade in his own image rather than following the traditional ways.
One possible plot could be that Adrien discovers some dark secrets about his family or the superhero world. Maybe he feels betrayed by Ladybug or the other heroes. This disillusionment could push him towards the dark side. For example, if he finds out that his father was a victim of the so - called 'good' superheroes' actions in the past, he might want revenge.
In a fanfiction where Naruto becomes a nukenin, it could be due to a prophecy that the village misinterprets. The village elders think Naruto will bring destruction, so they try to imprison or kill him. Naruto, not wanting to be a victim, escapes and becomes a nukenin. He then travels around, learning new jutsu from other lands and becoming stronger. Eventually, he might come back to the village to show them that their fears were unfounded, but by that time, he has become a very different ninja, with a new set of values and powers.
In such a fanfic, it might be due to a false accusation. Suppose Naruto is wrongly accused of a heinous crime like mass murder in the village. Everyone turns against him, and he has no way to prove his innocence. This overwhelming sense of injustice and isolation could drive him to suicidal thoughts. Also, if he discovers some dark secrets about his past, such as his parents' real cause of death being related to some sort of betrayal he unknowingly caused, it could break his spirit.
Perhaps in the fanfic, Cloud is on a journey to find himself and Zack is on a quest for justice. Their paths cross and at first they are at odds. But as they face challenges together, like dealing with a corrupt organization, they realize they need each other. Cloud provides the strategic thinking and Zack brings the brute force. And so, they become allies and friends.
Well, perhaps Merlin discovers a hidden magic that starts to transform him into a dragon. He might struggle with his new form, trying to control his dragon instincts like the urge to hoard treasure or fly away to a secluded lair.
Another idea is that Percy discovers he has a long - lost vampire heritage. As he becomes a vampire, he starts to unlock memories and powers related to his vampire lineage. He could go on a journey to find out more about his vampire ancestors and the secrets they held, all while adjusting to his new vampiric existence which is full of both challenges and newfound abilities.
In a 'sonic becomes a girl fanfic', the story could start with some kind of magical or scientific accident that turns Sonic into a girl. She then has to navigate her world with a new body. She may discover new abilities or limitations. Perhaps she teams up with female characters in the Sonic universe more often now and they form a strong girl - power group to take on the bad guys. There could also be a focus on how Sonic adjusts to her new appearance and how it affects her relationships with characters like Knuckles, who may have a different dynamic with her now.