Perhaps a fanfic where a crystal style user creates crystal clones that have different personalities and abilities. These clones could cause chaos in the village as they have a mind of their own. The main character then has to find a way to control them or face being exiled from the village. This would add an interesting dynamic as the character battles with their own power's unexpected side - effect.
One idea could be to change Naruto's initial upbringing. For example, instead of being shunned in the village, he could be secretly trained by an unknown shinobi who has a different view on the Nine - Tails. This would change his skills and how he approaches challenges in the ninja world. Another idea is to restart the story from the Chunin Exams but with different opponents and rules. It could add a new layer of excitement and unpredictability.
A cool plot for a Crystal Story 2 fanfic could be a story centered around a magical item that has been lost in the game world. The main character hears rumors about it and sets out on a quest to find it. Along the way, they face challenges from other characters who also want the item for their own reasons. It could also be interesting to write a fanfic about a character who gets cursed and has to find a way to break the curse while still dealing with the normal threats in the game world. Or perhaps a fanfic where two characters from different factions fall in love and have to overcome the differences between their groups.
Combining crystal style with water - style could be interesting. Maybe the user could create crystal formations that have water flowing within them. This could be used for both offensive, like shooting out jets of water - filled crystal shards, and defensive, by creating a moat - like barrier filled with water - encased crystals.
One idea could be a new character with ice style powers arriving in Konoha. This character could initially be seen as a threat but turns out to be an ally against a common enemy. Maybe an ancient ice - based evil is awakening, and only those with ice style can help stop it.
Another plot idea is that there's a secret group within the Naruto universe that has been experimenting with Titan shifting, and Naruto accidentally gets involved. He then has to figure out how to control this new power while also dealing with the group that wants to use it for evil. Maybe he discovers that some of his friends are also unknowingly part of this experiment, and he has to save them.
One idea could be that Naruto discovers a new and extremely powerful summoning scroll that allows him to call forth a god - like being from a forgotten realm. This being could teach Naruto a new form of chakra control that is far more advanced than what he has learned before.
A unique plot idea could be that Naruto's friends start to gain similar Saiyan - like powers. For example, Sasuke could develop a form that is a combination of his Sharingan and Saiyan power, which creates an interesting dynamic as they train together to master these new powers. Or perhaps, Naruto's Super Saiyan 3 form is the key to unlocking a long - forgotten prophecy in the ninja world that involves saving the entire universe from a cataclysmic event. In this way, the story could expand beyond the normal boundaries of the Naruto series.
A great plot idea could be centered around a moment in the history of the tailed beasts. For example, when the Sage of Six Paths first divided the chakra into the tailed beasts. It could show how the beasts were initially perceived by the world. Another idea is to look at a moment in the history of the Hidden Sand Village. Maybe during a time when they were at war with Konoha and the events that led to the peace treaties. You could also explore a moment in the history of the Sharingan, like how it was first discovered and developed within the Uchiha clan.
Some fanfictions have the idea of a character combining Fire Style with other elements in unexpected ways. For example, mixing Fire and Lightning to create a new, more powerful jutsu.
One idea could be a story where the Crystal Bearers have to team up with Naruto and his friends to stop a new, powerful enemy that is after the crystal powers. This enemy could be from a far - off land and have unique abilities that force the two groups to combine their skills.