One idea could be to explore Sigma's unique abilities in the Naruto universe. Maybe he has a special jutsu related to his Sigma nature. For example, he could have a jutsu that allows him to analyze and predict his opponents' moves with extreme precision, like how he might analyze data in his original context but now applied to combat in Naruto.
You could also create a fanfiction where Sigma teams up with some of the more underrated characters in Naruto. Together, they could form a sort of misfit group that goes on adventures and takes on missions that the regular ninja teams wouldn't. This would give a chance to develop both Sigma and those less - known characters in new and exciting ways.
One idea could be exploring how Ultron's advanced technology interfaces with Sigma's unique abilities. Maybe Ultron tries to assimilate Sigma's powers for his own evil plans.
One interesting idea could be the combination of Naruto's ninja skills with mecha technology. For example, Naruto might use his chakra to power up the mecha in unique ways. Another idea could be the new enemies that are created specifically for this mecha - Naruto concept, like robotic shinobi that require different combat strategies compared to normal foes. Also, the design of the mecha Naruto itself can be really cool, perhaps with features inspired by the Nine - Tails.
Another idea is that Aizen somehow ends up in the Naruto universe during the time of the Fourth Great Ninja War. He could try to manipulate both sides for his own gain. But Naruto, with his ability to see the good in people, might try to reason with Aizen and show him a different path. It could be a story of redemption or a great battle if Aizen refuses.
In a 'Naruto Mermaid Fanfiction', the mermaids could be in danger from an evil organization that wants to capture them for their precious scales. Naruto teams up with a mermaid princess to stop this threat and in the process, they learn about each other's worlds.
One idea could be a crossover where Naruto and Pucca end up in the same world due to a strange ninja jutsu gone wrong. Naruto is confused by Pucca's constant chasing of Garu, and he tries to help Garu escape in his own Naruto - style way.
Well, you could write a fanfiction where the Nine - Tails in Naruto has some sort of connection to a powerful entity in the Seraphim universe. This connection could lead to a series of events that require Naruto and the Seraphim characters to work together. Or perhaps a character from Seraphim is reincarnated as a ninja in the Naruto world and has to adapt to the new way of life while still having some of their Seraphim abilities.
One idea could be a blacksmith who creates unique ninja tools with special abilities that give the wielder an edge in battle. For example, a kunai that can change its shape during flight to avoid enemy defenses.
You could also write a fanfiction about Naruto being raised by a different clan in the village. For example, if he was raised by the Uchiha clan, it would have a huge impact on his character development and relationships within the village.
One idea could be that Krampus is summoned in the Naruto world during a particularly harsh winter. He mistakes the ninja villages for places full of naughty 'children' (in this case, ninjas who have misbehaved according to some warped view). Naruto then has to convince Krampus that the ninjas are actually good at heart and are just trying to protect their homes.
One idea could be that Naruto is somehow transported to the world of Athena. He might learn about her powers and the Greek mythology while also sharing his ninja skills. Maybe he could help Athena in a battle against a powerful enemy in her realm using his unique jutsus.