A simple way is to make Naruto encounter an orange - themed Pokemon event. For example, a festival in the Pokemon world that features orange - colored Pokemon like Flareon. Naruto gets involved in the festivities and through that, he meets new friends and gets into some light - hearted adventures.
In fanfiction, you can also combine their storylines. Say, the plot of 'The Lion King' could be merged with Naruto's journey to become Hokage. Simba's struggle to take his rightful place as king can be paralleled with Naruto's efforts to gain the respect of the Hidden Leaf Village and become its leader. There could be a common enemy that both Naruto and Simba have to face together, something that threatens both the pride lands and the ninja village.
The settings can be combined too. You could create a new world where the Naruto universe and the remnants of Krypton co - exist. Maybe there's a city in this new world where ninjas and Kryptonians live side by side. Naruto could then explore this new place, learn about Kryptonian technology, and use it to enhance his own ninja tools or techniques.
One way is to have the characters from Naruto join a peerage structure similar to that in Bleach. For example, the Hokage could be like the king of the peerage. Then, the jutsu of Naruto characters can be compared or integrated with the powers in Bleach. So, a Rasengan could be equivalent to a certain level of reiatsu - based attack.
The magic in Fairy Tail could be combined with Pokemon elements by having spells that are related to Pokemon types. For instance, a water - mage could use a spell to create a Pokemon - like water creature. Or a lightning - mage could summon an electric - type Pokemon - inspired bolt of energy.
Well, for starters, Sasuke's Sharingan could be used to analyze Pokemon moves and weaknesses quickly. It would give him an edge in battles. His ability to control fire could also be combined with a Fire - type Pokemon's attacks to make them more powerful.
Another way is to have Naruto fuse his chakra with someone who has the ability to use Susanoo, like Sasuke. They could create a combined form that has the best of both their powers. The story could detail their journey of learning to work together and master this new form.
Well, one way could be that the chakra in Naruto's world is similar to the energy that Pokemon use. So, a Pokemon might be able to absorb chakra to become stronger. Or a ninja could learn to use Pokemon energy to enhance their jutsu. For example, a fire - style jutsu could be powered up by the energy of a fire - type Pokemon.
One way to combine them could be through a crossover device. For example, a powerful Pokemon like Mewtwo could accidentally open a portal to the Avengers' universe. Then, the Avengers might mistake the Pokemon for some kind of new alien threat. They would try to contain it, but soon realize that the Pokemon has no malicious intent. Meanwhile, the Pokemon trainer who follows Mewtwo through the portal has to team up with the Avengers to find a way back home and also deal with any villains in the Avengers' world that might try to use the Pokemon for their own gain.
You can have characters like Ash from Pokemon become a part of the Star Wars universe. He could be a young Force - sensitive being who uses his knowledge of Pokemon to his advantage. For instance, his Pokemon could help him in starship battles or in exploring new planets.
Their abilities can be combined in a rescue mission. For example, if there are Pokemon trapped in a cave. Sountland can sniff out the exact location of the trapped Pokemon from outside the cave. Flygon can then use its digging ability (if we assume it has some) along with its flying to enter the cave from above and clear the way for the rescue. This would show how their different abilities work together for a common goal.