One possible plot could be that Naruto and his friends are transported into the Resident Evil universe. They team up with some of the Resident Evil survivors to fight against the zombies and bio - organic weapons. Naruto could use his shadow clones to distract the hordes of zombies while the others find a way to develop a cure using Naruto's chakra which has some unique properties.
One possible plot could be that James Heller somehow gets transported into the Resident Evil universe. He then has to team up with the Resident Evil characters to fight against a new and powerful virus that is a combination of his world's threats and the Resident Evil ones.
One idea could be that Naruto and his team are sent to the Resident Evil universe to find a cure for a virus that has started to infect the Hidden Leaf. They would have to face off against zombies and bio - weapons using their ninja skills. Another plot could involve a Resident Evil character getting transported to the Naruto world and having to adapt to chakra and ninja society. For example, Leon Kennedy could team up with Naruto to stop a bio - terrorist attack in Konoha.
A possible plot is that some of the characters from Naruto are experimented on by the Umbrella Corporation. Sasuke, for instance, could have his Sharingan enhanced in unexpected ways due to the unethical experiments. This would lead to a power struggle within him as he tries to control his new abilities while also dealing with the fact that he has been turned into a sort of bio - weapon. And then Naruto would have to find a way to save him without getting infected himself.
One idea could be that Lara Croft is exploring an ancient tomb and stumbles upon a hidden Umbrella Corporation facility. She discovers that they were experimenting with some sort of ancient virus that was sealed in the tomb long ago. The T - virus has escaped and is starting to mutate the local wildlife and some of the tomb's guardians. Lara has to team up with a Resident Evil character, like Jill Valentine, to stop the virus from spreading further and also figure out how to deal with the newly awakened threats in the tomb.
A plot could be set where the Black Light virus is used as a weapon against the bio - weapons of Resident Evil. A group of survivors discovers the Black Light's potential to neutralize some of the more dangerous Resident Evil creations. However, they soon realize that controlling the Black Light is just as difficult as controlling the Resident Evil viruses, and they face new threats as a result.
One possible plot could be that a bio - hazard outbreak occurs in New York City. Spiderman has to not only fight the usual criminals but also deal with the infected. Meanwhile, some Resident Evil characters like Leon S. Kennedy are sent to investigate the outbreak. They cross paths with Spiderman, and at first there is mistrust, but they soon realize they need to work together to stop the spread of the virus and take down the mastermind behind it, perhaps a new villain who has combined Oscorp technology with Umbrella Corporation's bio - weapons.
Another interesting twist is if it turns out that some of the powerful jutsu in the Naruto world are actually the result of an ancient experiment similar to the ones in Resident Evil. For example, the Sage of Six Paths was actually trying to create a powerful being by combining natural energy with a virus - like substance, which is similar to how the Resident Evil scientists create their monsters. This revelation could change how the Naruto characters view their own powers and history.
Well, a cool fanfiction concept could be that some of the Resident Evil villains get transported to the Naruto universe. For example, Albert Wesker shows up and tries to take over the ninja villages using his superhuman abilities and intelligence. Or perhaps the Resident Evil bio - weapons are let loose in the Naruto world and the shinobi have to figure out how to deal with these new threats that are completely different from their usual enemies like other ninja clans or rogue ninjas.
A crossover could involve the T - Virus from Resident Evil 2 affecting some of the Naruto world. Imagine some ninja getting infected and turning into zombie - like creatures with ninja abilities. This would create a whole new level of threat. The Konoha ninja would then have to figure out how to deal with this new type of enemy. They might use their jutsu in combination with Resident Evil - style weapons and strategies. For instance, Sakura could use her medical ninjutsu to try to find a cure for the T - Virus while also using a gun she found in Raccoon City.
It could be really interesting. Picture Naruto in the spooky world of Resident Evil 7. He might use his ninja skills to fight off the molded. His shadow clones could be used for distractions while he figures out how to deal with the Baker family. Maybe he'd use his rasengan against the grotesque creatures, creating a whole new dynamic to the Resident Evil 7 story.