One idea could be that Naruto discovers the Bakugan world during one of his training journeys. He meets Alice and they team up to fight against an evil force that is trying to take over both the ninja world and the Bakugan world. Naruto's ninja skills combined with Alice's knowledge of Bakugan could make for an interesting story.
Well, it could be about Naruto somehow getting involved in the Bakugan world. Maybe he discovers Bakugan while on one of his missions in a strange new land. He might form an alliance with the Bakugan and their human partners to fight a common enemy, like an evil force that threatens both the Ninja world and the Bakugan universe.
Maybe Naruto discovers Bakugan during one of his travels outside the Hidden Leaf Village. He could be intrigued by the unique powers and battles of Bakugan. He might start collecting them and use his ninja skills to master the Bakugan battles, making new friends in the Bakugan world who are also impressed by his ninja abilities.
Create interesting plotlines. You can start with a simple premise like a portal opening between the two worlds and then build on it. Incorporate elements from both Naruto and Bakugan. Maybe there's a mission to find a lost Bakugan in the Naruto world. Also, don't forget about character development. As the story progresses, the main character and the harem members should grow and change. This could be in terms of their relationships, powers, or worldviews.
Well, a cool plot could be that the Bakugan come from a parallel dimension and are used by an evil organization to invade the Naruto world. Naruto then teams up with some friendly Bakugan to fight back. There could also be a plot where Naruto's chakra has an unexpected interaction with the Bakugan, giving them new and powerful abilities. He then has to train with these enhanced Bakugan to face a powerful foe that threatens both the Naruto world and the Bakugan world.
Obviously Naruto would be one of the main characters. Since it's a crossover, characters from Bakugan like Dan Kuso would probably be in it too. Maybe Sasuke could also be involved, as he often follows Naruto's adventures in some way. And of course, there would be the Bakugan themselves, like Drago or Pyrus. They would play important roles as partners to the human characters.
One popular Naruto and Bakugan fanfiction is 'The Ninja's Bakugan Adventure'. It combines the unique abilities of Naruto characters with the Bakugan battle system in an exciting way.
A third popular trope is the 'forbidden love' aspect. Maybe a relationship between a Naruto character and a Bakugan - related character is frowned upon in their respective worlds. This adds an element of drama and tension to the fanfiction. For example, if a shinobi from Naruto falls in love with a Bakugan trainer, their different cultures and duties might create obstacles for their relationship.
Another interesting plot twist is when the main villain in the Naruto world turns out to be in cahoots with an evil Bakugan from another dimension. This forces Naruto to not only fight his regular enemies but also understand the complex politics and power struggles in the Bakugan world to stop the greater threat. It's a really cool way to merge the two universes.