Well, it could be that there's a plot device like an ancient artifact. This artifact might have the power to draw out and combine the Akatsuki powers. The Akatsuki members themselves might be tricked into contributing their powers to this artifact, and then the protagonist or an antagonist gets hold of it and gains all those combined powers. It's a common trope in fanfiction to use such magical or mysterious items to bring about extraordinary power combinations.
One potential consequence could be a shift in the power balance. Naruto was already a strong force, but with Akatsuki powers, he could become nearly unbeatable. This might make other villages either fear him or try to ally with him more strongly. Enemies of Konoha might think twice before attacking. Also, the Akatsuki's powers often come with a certain darkness, so Naruto might have to struggle with that aspect of his new abilities.
It could be the main protagonist if the story is written in a way that the character manages to control and utilize all the Akatsuki powers effectively. With the combined powers, they would have a vast array of abilities at their disposal, making them extremely formidable.
Well, if Naruto had Akatsuki powers in fanfiction, it could make the story way more intense. He might be able to use some of the Akatsuki's really cool and dangerous jutsus. For example, he could use Pain's rinnegan abilities to quickly defeat enemies. This would change the power balance in battles. Also, it could lead to a different relationship with other characters. Some might fear him more, while others could try to use his new powers for their own gains.
Pain's rinnegan power would be an amazing addition for Naruto. The rinnegan has so many abilities like the six paths. Naruto could use these powers to better understand the world and help people on a larger scale. He could use the power of the Deva Path to manipulate gravity, which would be useful in both combat and for things like building infrastructure in the village. Also, the rinnegan's connection to the afterlife could give Naruto new insights into the spirits and souls, which could be relevant in his interactions with the Nine - Tails and other spirits in the Naruto universe.
Well, if Naruto has Akatsuki powers in the fanfiction, his combat style might become more stealthy. Akatsuki members are often associated with sneaky tactics. He could use some of their jutsu like the Sharingan - if he were to somehow get that power - to predict his opponents' moves better, which is a big change from his more straightforward, brute - force - with - Rasengan - type combat style.
Since the Akatsuki often deals with sealing techniques, Naruto's skills with the Nine - Tails' seal could be enhanced in a different way. He might learn to better control the Nine - Tails' power without relying on the methods taught in Konoha. Also, his physical abilities could be trained differently. Maybe he'd focus more on speed and stealth, which are qualities often valued by the Akatsuki.
One possible place to find such a fanfiction is Archive of Our Own. They have a large collection of Naruto - related fanfictions, and this specific plot might be there. Just use the search bar and type in 'akatsuki find a baby with special powers' and see what comes up.
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.
Well, in this fanfiction, it could be that Akatsuki has a change of heart. Some members might realize that Naruto represents a hope for the ninja world in a different way than they initially thought. So they step in to save him when he's in a really tough situation, like being trapped in a powerful jutsu or surrounded by a large number of enemy ninjas. They use their own unique skills, like Kisame's water jutsu or Itachi's Sharingan abilities to fight off the threats.