In some fanfictions, Naruto might have the power to control time. For example, he could freeze time during battles to gain an advantage. Another impossible power could be the ability to instantly teleport to any location in the ninja world without using any known jutsu. He might also have the power to communicate with all living beings telepathically, which is not part of his original abilities in the official story.
Well, often they use the idea of Naruto's strong will. They say that his will is so strong that it breaks the normal limits of what is possible in the Naruto universe. So, his will allows him to access these impossible powers. Also, in some fanfictions, Naruto goes through some extreme and unique training or experiences that no one else has had, and this is what gives him these extraordinary abilities. For example, he might travel to a different dimension where the laws of physics and chakra are different, and when he comes back, he has these new powers.
In this fanfiction, the prototype powers could be something like an early form of chakra manipulation that is different from the traditional Naruto world's chakra use. It might be more raw and unrefined, with the potential for new and unique jutsu.
His hidden powers might be the ability to control all five basic nature types without any training. In the original story, Naruto had to work hard to master different nature types. But in a fanfiction, it could be that he has this innate ability which was hidden all along. This would make him extremely powerful and feared by his enemies.
In some fanfictions, Naruto's multiverse powers are portrayed as a way to bring together different versions of himself. Each version has its own set of skills and knowledge. By merging these aspects, he becomes an even more powerful and complex character, able to solve problems that were previously insurmountable.
Well, he could use Freddy's power of entering people's dreams to fight his opponents in the dream realm. Maybe he would trap his enemies in a never - ending nightmare, causing them mental distress and weakening their will to fight in the real world.
He could have enhanced physical abilities. Since yokai are often known for their strength and speed, as the King of Yokai, Naruto might gain even greater strength and faster reflexes. He may also have the ability to communicate with all types of yokai, understanding their languages and thoughts, which would give him an edge in dealing with them.
Well, Naruto would become extremely powerful. He could use Sinbad's magic powers along with his own ninja skills. Maybe he could fly around the Hidden Leaf Village like Sinbad on his magic carpet and use his powers to protect the village in ways he couldn't before. It would be a really cool combination.
Often, Orochimaru remains an antagonist even in these fanfictions. His thirst for power and immortality makes him a natural foe for Naruto, especially when Naruto has new super powers to protect. Another common one could be Madara Uchiha, as his grand plans for the world are likely to clash with Naruto's newfound abilities and his desire to protect peace.
In some fanfictions, Naruto might gain the ability to control energy like a laser beam which is an alien - like power. For example, he could shoot beams from his hands to defeat enemies.