There are quite a few ways actually. He could be blessed by a god - like being in the fanfiction world. This being could see his potential and give him the gift of flight to help him in his quests. Or perhaps he discovers a hidden power within himself that has been dormant all along. This power could be related to his Uzumaki heritage, and once awakened, it gives him the ability to fly. Some fanfictions also suggest that he could use a combination of his shadow clones and some special chakra - based technique to create a flying platform or something similar to fly on.
In some fanfictions, Naruto could gain the ability to fly as a result of a forbidden jutsu. This jutsu might be so powerful that it not only gives him flight but also enhances his other abilities. For instance, he could be forced to use this jutsu in a life - or - death situation against a very powerful enemy. Also, he could fly if he absorbs some kind of special energy or power - up from an ancient relic. This power - up could transform his body in a way that allows him to fly, like growing wings made of pure chakra.
One way is through brute force. Houndoom could be extremely powerful in the fanfiction and simply overpower Naruto's attackers. For instance, if there are some assassins after Naruto, Houndoom could charge at them and knock them out with its physical strength.
One way is by using his Sage Mode. Naruto in Sage Mode has enhanced senses and chakra control. He could use these advantages to refine the Hiraishin. For example, he might be able to make more precise teleportations or detect potential threats at the destination of the Hiraishin more accurately.
Naruto could use Ki to enhance his sensory abilities. In the Naruto universe, he already has good sensory skills with his chakra. But by adding Ki into the mix, he could expand his range of detection even further. He could sense enemies from much greater distances or even detect hidden traps or secrets in the environment around him.
Well, Naruto could have a special kekkei genkai (bloodline limit) in fanfiction that enables him to manipulate metal. This could be something he discovers later in life. He could use this ability to create metal barriers for protection, or he could use it to launch a barrage of metal shards as an attack. He might also be able to merge with metal, like some sort of metal - ninja hybrid, and gain enhanced strength and durability while being in that form.
One way could be that Naruto sacrifices himself to defeat a powerful enemy like a new Akatsuki member. His friends, using some ancient jutsu they discover, manage to revive him. For example, Sakura might find a scroll in an old temple that details a revival technique.
One way could be through a power - sharing ritual. In fanfiction, an Uchiha character might willingly share their Sharingan and the potential for Susanoo with Naruto. Another way is if Naruto somehow taps into an ancient power source that contains the essence of the Uchiha's abilities, including Susanoo.
One way is by his words. Naruto is known for his passionate speeches. In fanfiction, he could use his powerful words to stir up emotions that lead to chaos. He might speak out against unfair treatment or corruption, causing a stir among the villagers and ninja, which then results in a chaotic situation as people start to act on their new - found beliefs.
In fanfiction, Naruto may also use chaos energy for defensive purposes. He could form a chaos - energy - based shield around himself. This shield would not only protect him from physical attacks but also from enemy jutsu. The chaos within the energy would disrupt and disperse incoming attacks, making it a very effective defensive technique.
In fanfiction, Naruto might figure out the bell test by observing Kakashi's behavior closely. He might notice that Kakashi is not really trying to stop them from getting the bells but rather is observing how they interact. Naruto could then think that the real test is about how they handle the situation as a team. He could start to initiate conversations with his teammates about their goals and how they can achieve them together. By doing this, he shows that he has grasped the concept behind the bell test, which is to build a strong and cohesive team through mutual understanding and cooperation.
One way could be that Naruto experiences a great loss, similar to Obito losing Rin. This loss could make him question the ninja world and its values, leading him to take a darker path. For example, if he lost Hinata in a cruel way, it might shatter his positive view of the world.