A new, self - created android by Dr. Gero's successor could be the main villain. This android could be specifically designed to target and defeat Super Saiyan Blue users. It could have the ability to absorb their energy and use it against them, making it a very difficult enemy for Goku and Vegeta to face.
One idea could be a story where the Saiyan Blue form has an unexpected side effect. For example, it could start to drain the user's life force slowly but surely. Goku discovers this during a battle and has to find a way to either control it or reverse the effect while still fighting powerful foes.
Another plot could be that a mysterious entity bestows the power of Super Saiyan Blue on Naruto. He then has to keep it a secret from his friends and village while also using it to protect them from a new and powerful enemy. This would create a lot of internal conflict for Naruto as he tries to balance secrecy and heroism.
One great Super Saiyan Blue Goku crossover fanfiction is 'Goku in the DC Universe'. It's really exciting to see Goku interact with Superman and other DC heroes. He has to adjust to the different power levels and rules in that universe.
Sure does. Goku attains the perfected SSJB in the manga during intense battles and as part of his power-up journey. It's a significant moment for his character development.
A Super Saiyan in Naruto fanfiction could be a result of a dimensional rift. Maybe a portal opens between the Naruto and Dragon Ball universes and some Saiyan energy seeps through, affecting a Naruto character. This would be an interesting plot device as it would introduce an alien concept to the ninja world.