One idea could be that the characters from Sister Location end up in an alternate universe where they have to team up with the original FNAF characters to fight a new, more powerful animatronic threat. This would bring a lot of interesting character dynamics as they try to figure out each other's motives and abilities.
A plot could involve a time - travel aspect in the fanfiction. The main character from Sister Location accidentally travels back in time to when the first FNAF pizzeria was being built. They then have to use their knowledge of the future animatronics to prevent some dark events from occurring, while also trying to find a way back to their own time. This would allow for a lot of exploration of the FNAF lore from different time periods.
Maybe the animatronics in Sister Location are infused with chakra due to some strange experiment. Naruto senses this and tries to understand how to use this new form of chakra. He might have to team up with some of the more 'friendly' animatronics to stop a greater evil that is threatening both the Naruto world and the FNAF world.
One idea could be exploring the backstories of the animatronics in more depth. For example, creating a story about how the Ballora was created and what her purpose was originally supposed to be. Another could be a time - travel fanfic where a character goes back in time to prevent the disasters at Sister Location from happening. And a third could be a story centered around the relationship between the different animatronics, like a friendship or rivalry between Funtime Freddy and Circus Baby.
One idea could be that Foxy from FNAF crosses over into another universe where he teams up with a group of unlikely heroes. Maybe he uses his speed and stealth to help them in a battle against a common enemy.
One plot idea could be that the characters from MyStreet end up in the FNAF pizzeria. They initially think it's just a strange place but soon realize the danger of the animatronics. Another idea is that the FNAF animatronics somehow enter the MyStreet world and start causing chaos among the peaceful MyStreet community. For example, Freddy might try to take over the local diner in MyStreet, thinking it's his territory.
A possible plot could involve the souls in Undertale having some connection to the spirits that are rumored to be in the FNAF animatronics. The main character from Undertale, perhaps Frisk, could enter the FNAF world and try to free the trapped souls. In return, the animatronics could help Frisk in the Undertale world against some powerful foes.
Well, it could be that there is a glitch in the multiverse that causes a fusion of the two worlds. So we have characters like Frisk interacting with Freddy Fazbear. Frisk might try to show the animatronics a different way of living, more like the pacifist way in Undertale. And in the process, they all have to deal with the threats that exist in both worlds, like the purple guy from FNAF and the more malevolent monsters from Undertale.
There are fanfictions that explore the idea of Baby having a conscience and trying to break free from her programmed actions. For example, she might start to question why she has to do certain things like luring people. In some fanfictions, Baby also has memories that she tries to piece together, which makes for a very engaging read as we discover more about her past along with her.
It could be a new, super - intelligent animatronic created by combining the technology from both Sister Location and the original FNAF series. This animatronic would have all the worst traits of both, like the stealth of the Sister Location ones and the aggression of the original ones.
One idea could be that the characters from Gravity Falls end up in the FNAF world. Dipper might be intrigued by the mystery of the haunted animatronics and try to solve it using his journal. Mabel could befriend the more friendly - looking animatronics, like Chica, and try to make them cute accessories. Another plot could involve the FNAF villains getting loose in Gravity Falls and the Pines family having to use the town's unique magic to stop them.
One idea could be that Sonic and his friends accidentally end up in the FNAF universe. Sonic's speed could be a huge advantage against the animatronics. For example, he could quickly dash around the haunted pizzeria, confusing the animatronics and leading them into traps. Another idea is that the animatronics from FNAF somehow get transported to Sonic's world. The chaos that would ensue as they try to adapt to the bright, colorful and fast - paced Sonic world would be really interesting to write about. Maybe Sonic and Tails would have to figure out a way to send them back while also protecting their friends from the animatronics' unpredictable behavior.