Well, perhaps the Akatsuki members in Naruto are seen as a powerful guild in the World of Warcraft. They could be on a quest to obtain some powerful artifacts in WoW, like the Ashbringer. And Naruto and his friends have to stop them. Or, imagine the tailed beasts in Naruto being mistaken for powerful elemental spirits in WoW, and different factions try to either control or destroy them.
A really cool plot idea could be that the shinobi world discovers the World of Warcraft and decides to send some of their best, including Naruto, to learn about their magic and technology. In WoW, Naruto meets Thrall and they form a bond. Thrall teaches Naruto about shamanism, which Naruto then combines with his own chakra control, creating a new form of combat. Meanwhile, Sasuke might be intrigued by the power of the Death Knights and gets into some dangerous situations trying to understand their power source.
One idea could be that Naruto characters are transported to the World of Warcraft universe. They could form alliances with different races like the Night Elves, with Naruto's ability to befriend others coming in handy. Another could be that the chakra system in Naruto somehow interacts with the magic in WoW, creating new and powerful spells.
Well, perhaps there's a plot where the World of Warcraft is in danger of being overrun by an evil force similar to the Otsutsuki in Naruto. The Naruto characters are called upon to help because of their unique abilities. Sakura could use her medical ninjutsu to heal the wounded in WoW, and Kakashi could lead strategic battles. The ninjas would have to adapt to the different terrains and cultures of WoW while using their own skills to turn the tide against the common enemy.
Perhaps a group of Azeroth's heroes, like the Night Elves or the Dwarves, stumble upon a Halo ring. They have to figure out the technology there while also facing threats from the Covenant. The mages could try to understand the Forerunner magic-like technology, and the warriors would engage in combat with the alien foes.
Well, a great plot for a Naruto Uchiha crossover fanfic could be centered around time travel. Imagine Naruto going back in time and trying to prevent the Uchiha massacre. He could use his knowledge of future events and his own unique skills to change things. Or perhaps an Uchiha character, say Sasuke, gets sent to a future where Naruto has become Hokage and they have to work together to solve a new, greater threat to the ninja world that is beyond what they've faced before. There could also be a plot where Naruto and an Uchiha are magically bonded and have to share their emotions and powers, which leads to a whole new dynamic in their relationships and how they face challenges.
One idea could be Naruto being reborn into the world of One Piece. He could use his ninja skills to navigate the Grand Line. Maybe he'd form an alliance with the Straw Hat Pirates and teach them some unique jutsu in exchange for learning about Haki.
One idea could be that Naruto characters are transported to the RWBY world. Naruto himself could befriend Ruby and they could learn from each other's combat styles. For example, Naruto's chakra control might inspire Ruby to better control her own energy. Another plot could involve the Akatsuki from Naruto being interested in the Dust in RWBY's world and causing chaos to obtain it.
Well, a plot could revolve around a Rinnegan - induced time - loop situation. A character, perhaps Sasuke, gets caught in a time - loop where he has to keep reliving a certain period in the Naruto story but with different outcomes each time due to the influence of the Rinnegan. He has to figure out how to break the loop and in the process, discovers new secrets about the Rinnegan and its origin. This could also lead to him changing the fate of some characters who died in the original story.
One idea could be that the Hogwarts students are transported to Azeroth. They could learn magic from the Warcraft mages while also sharing their own spells. For example, Hermione might be fascinated by the arcane magic in Warcraft and try to find similarities with her own knowledge of magic. Another plot could involve Voldemort teaming up with an evil force from Warcraft to conquer both worlds. Harry and his friends would then have to gather allies from both universes to stop them.
Perhaps there could be a hidden shinobi village in Pompeii that was wiped out during the eruption. Naruto discovers ancient scrolls in Konoha that lead him to Pompeii, where he uncovers secrets about a lost ninja clan and their unique jutsu that could help him in his fight against a new threat in his own time.
A crossover with 'Steven Universe' would also be cool. Gumball and Steven could bond over their unique family situations. They could have to use the power of friendship, Gumball's wacky schemes, and Steven's gem powers to defeat a common enemy, like an evil gem who wants to turn Elmore into a gem colony.
One idea could be a crossover of the two universes' races in a battle for a powerful, ancient artifact. For example, the Orcs from Warcraft and the Orks from Warhammer could form an uneasy alliance against a common enemy like a powerful demon lord that threatens both worlds.