One idea could be exploring how Naruto discovers a new way to enter Gear Second that gives him even more power. Maybe he combines it with a new jutsu he's been working on.
Maybe a plot where Naruto uses Gear Second in a completely unexpected situation, like during a diplomatic negotiation that goes wrong. His sudden display of power could change the course of the negotiation and the relationships between the villages involved. He might have to deal with the consequences of showing such a powerful form in a non - combat setting.
For a Luffy Gear 5 fanfic, you could have a plot where Luffy's Gear 5 form is somehow corrupted by a dark force. He starts to lose control of his actions and becomes a danger to his friends. His crew has to find a way to purify his Gear 5 power. Another interesting idea is that Luffy discovers that Gear 5 has a hidden ability that allows him to travel through time briefly. He uses this ability to go back and change a crucial event in the past that has far - reaching consequences for the present. This could lead to a whole new set of adventures and challenges for Luffy and his crew.
One idea could be Naruto obtaining the Boosted Gear and using its power to enhance his shadow clones. The clones could then have a unique power boost that gives them an edge in battles. Another could be Naruto using the Boosted Gear's abilities to travel between dimensions, leading to encounters with different versions of himself.
One idea could be that Naruto gets a second chance at life but in a different ninja village. He has to adapt to new rules and make new friends while still carrying his past experiences. For example, he might end up in the Sand Village and learn their unique jutsu.
One idea could be that Percy discovers a new kind of Sacred Gear during one of his quests. Maybe it has the power to control water in a completely different way than his normal abilities. Another could be a crossover where Percy and a character with a Sacred Gear team up to defeat a common enemy that neither could face alone.
One idea could be a crossover where the characters from Metal Gear Rising have to adapt to the world of RWBY. For example, Raiden could team up with Ruby and they could share their combat skills. Maybe Raiden teaches Ruby some advanced sword techniques, while Ruby shows Raiden how to use Dust in combat.
Perhaps in the fanfiction, the Akatsuki somehow gets hold of the knowledge of Gear Fourth - like power and tries to use it against Naruto. Naruto then has to quickly master this form to not only defeat the Akatsuki but also prevent them from misusing this power for evil purposes. This could lead to some intense battles and strategic showdowns.
A really interesting plot could revolve around the Second Hokage's relationships. For example, his relationship with the other clans in the village. He might have to deal with the Uchiha clan's growing unrest. This could lead to him making difficult decisions to maintain the peace in the village. He could also have a mentor - mentee relationship with a young and talented ninja, guiding them to become a great shinobi.
Perhaps a story where some of the Metal Gear technology finds its way into the Naruto world. Orochimaru might be interested in getting his hands on such advanced tech for his experiments. He could try to reverse - engineer it to enhance his own abilities or create new, powerful jutsu. And Konoha would have to deal with the threat of this new, unknown technology while also facing their regular enemies.
Some fanfics might focus on the relationships between the characters. For example, a story could explore a romantic relationship between two air gear riders. This would not only show their love story but also how their relationship affects their performance in the air gear battles and their standing in the air gear community.