One unlikely ally could be Zetsu. Zetsu is usually seen as a villain, but in a fanfic, he could have his own motives for helping Naruto defeat Pain. Maybe he wants to disrupt the Akatsuki's plans from the inside and sees Naruto as a useful tool for that.
Tsunade might be an unlikely ally in a different way. Usually, she's more of a support figure in the background. But in a fanfic, she could directly join Naruto in the fight against Pain. She could use her medical ninjutsu not just for healing but also in an offensive way, like creating chakra - infused attacks that catch Pain off - guard.
Sasuke could also be an unlikely ally. Given their complicated relationship, in a fanfic, Sasuke could realize that Pain is a greater threat to the ninja world as a whole. So, he decides to put aside his differences with Naruto for the time being and help him defeat Pain. This would create an interesting dynamic between the two characters during the battle.
In this fanfiction, Naruto might find Tiny Tina's love for chaos and destruction a bit overwhelming at first. But he would soon realize that her wild nature can be an asset. For example, when they are facing a horde of enemies, Tiny Tina could create a distraction with her crazy antics while Naruto slips in unnoticed to take out the leaders. It would be a story of two very different characters learning to work together and becoming friends in the process.
Yes, they could be unlikely allies. Naruto's superhuman abilities from being a ninja and Jessica's detective skills and super strength could combine in a unique way. Maybe Naruto needs help finding a missing person in Jessica's world, and she enlists his help because of his tracking skills. Together, they would make a formidable team.
In some fanfics, Naruto might team up with unexpected characters to defeat Pain. For example, he could join forces with Orochimaru. Orochimaru, with his knowledge of jutsus and dark arts, and Naruto, with his brute strength and positive energy, create a unique combination that outsmarts Pain's abilities.
In a Naruto and Satsuki heroic spirit fanfiction, their alliance could lead to some really interesting character interactions. Naruto might try to break through Satsuki's cold shell and make her see the good in the world again. Satsuki, on the other hand, could teach Naruto some more refined combat techniques. Their different personalities would create a lot of friction at first, but as they face more challenges together, they would start to understand and respect each other more. And this newfound respect could be the key to their success in fighting the common enemy.
A fanfiction could involve Naruto and Jennifer Lawrence teaming up to save a world that is a blend of their two universes. They might have to face challenges that require both Naruto's combat skills and Jennifer Lawrence's acting skills (in a more metaphorical sense, like using her ability to play different characters to deceive enemies).
In this fanfic, Agumon might be a loner Digimon who is used to fighting on his own. Biyomon, on the other hand, is more community - oriented. When they first meet, they don't get along. But as the threat grows, they start to see the value in each other. Agumon learns about the importance of teamwork from Biyomon, and Biyomon learns to be more assertive from Agumon. Their partnership evolves over time as they face different challenges together.
Kakashi could still be an important ally even though Naruto has become a Jounin. Kakashi has a wealth of experience and knowledge that Naruto could still learn from. He could offer advice and assistance when Naruto faces tough challenges in his new role.
Shego and Kim as unlikely allies could mean that they are brought together by fate. Perhaps a powerful artifact is about to be misused, and they are the only two who know how to stop it. Their initial meetings would be full of tension, but as they start to understand each other's motives, they form a tentative bond.
A Batman x Atwoman fanfic could also focus on the emotional side of their relationship. Imagine Atwoman has a personal vendetta against a particular villain. Batman initially doesn't understand why she is so obsessed. But as he gets to know her story, he realizes that it's similar to his own quest for justice. This understanding brings them closer. They start to share their feelings and fears, and this newfound emotional bond helps them become even stronger allies when facing the challenges in their cities, whether it's fighting gangs or stopping mad scientists.
Bayleef and Latias make for an interesting pair in a fanfic. They could start as unlikely allies. Maybe Bayleef is initially afraid of Latias because of her dragon - like appearance and psychic powers. But as they are forced to work together to solve a mystery in their Pokemon world, like the disappearance of a certain type of Pokemon, they gradually start to trust each other.