How about the idea of the ninjas from Naruto trying to find a way to reverse the radiation in Fallout 4? They could use their chakra knowledge and skills. Hinata could use her byakugan to detect sources of radiation more accurately. And Naruto could use his positive energy and willpower, which is often associated with his chakra, to try and purify some of the polluted areas.
One idea could be a character from the Enclave finding themselves in a situation where they have to team up with a group from the Fallout world they usually oppose. Maybe a lone Enclave soldier gets separated from his unit and is forced to rely on a group of wastelanders to survive. This could lead to a lot of character development as he sees a different side of the world outside the Enclave's ideology.
A lesser - known but really engaging one is 'Female Courier: Beyond the Wasteland'. Here, the female courier crosses over into a more technologically advanced part of the Fallout world that she's not familiar with. It delves deep into her character development as she struggles to understand and survive in this new area. There are some great plot twists along the way.
A plot could involve a group of settlers from Fallout 3 trying to make a new start in the Mojave. They run into trouble with the various factions in New Vegas. Meanwhile, a character from New Vegas goes to the Capital Wasteland to learn about their different ways of survival. This leads to an exchange of ideas and technology between the two groups, as well as some clashes due to different values.
A crossover could involve Tohru from Dragon Maid being interested in the ninja way. She could travel to the Naruto world and try to become a ninja herself. She'd be a very powerful addition with her dragon abilities. She could also introduce some of the unique things from her world, like her cooking, to the Naruto characters.
One idea could be that the characters from RWBY end up in the Fallout wasteland. Ruby could use her scythe skills to fight off raiders and mutants. Weiss might use her glyphs to protect the group from radiation in certain areas. Another idea is that the Dust from RWBY could be a valuable resource in the Fallout world, leading to various power struggles.
One idea could be that the Dragonborn from Skyrim somehow gets transported to the post - apocalyptic world of Fallout 4. Maybe they have to deal with the new threats like the raiders and mutants using their dragon - slaying skills. Another plot could involve the Sole Survivor from Fallout 4 finding a way into Skyrim and getting caught up in the civil war there, having to choose a side while also trying to find a way back home. Or perhaps a magical artifact from Skyrim ends up in Fallout 4 and causes all kinds of chaos as different factions fight over it.
One idea could be a character from Fallout finding themselves in Skyrim. Maybe they bring their advanced weaponry, like a laser pistol, into Skyrim's medieval - like world. This would cause quite a stir among the locals, who have never seen such technology. The character could then get involved in Skyrim's political intrigue, using their unique skills to help or hinder different factions. Another plot could involve a Skyrim mage traveling to the Fallout wasteland. They would be amazed by the strange, post - apocalyptic magic (technology) there and try to learn about it, while also using their own magic to survive against the mutated creatures.
One idea could be to cross the Sole Survivor with a character from another post - apocalyptic game like Metro. The Sole Survivor could bring their unique skills and knowledge from the Fallout universe into the Metro tunnels. They might have to deal with different kinds of mutants and a more claustrophobic environment. It would be interesting to see how they adapt and interact with the Metro characters.
One idea could be that Guts from Berserk is somehow transported to the Naruto universe. He could encounter Naruto and his friends. Maybe they initially mistake him for an enemy because of his intimidating appearance and weaponry. But as they get to know him, they realize his noble heart and his fight against the forces of evil in his own world, and they team up to face a common threat in the Naruto world.
One idea could be that the Tenno from Warframe are summoned to the Naruto universe during a great war. They could use their advanced technology and unique abilities to help the ninja clans. For example, the Excalibur could use his Radial Javelin ability to clear out large groups of enemy ninjas, much like a powerful ninjutsu.