In general, the Akatsuki no Yona anime didn't fully catch up to the manga. There are still significant parts of the story in the manga that weren't included in the anime adaptation. Maybe it was due to various production considerations or limitations.
The number of death episodes of Akatsuki's members in the Naruto anime are as follows:
1 Dedale:35 episodes
2 Scorpions:36 episodes
3 Flying Steps:10 episodes
4 Corners:13 episodes
Orochimaru:19 episodes
6. Members of Shinobu Village (including Shinobu Village's captain, Jingyin):22 episodes
7 I Love Luo:54 episodes
8:69 episodes
9 Flying Apes:73 episodes
It should be noted that these episodes were not the ones where all the members of the Akatsuki organization died.
Naruto is a Japanese manga and cartoon that tells the story of a ninja world. Among them, Akatsuki was an important organization composed of Payne, Itachi, Sasuke, and others. Akatsuki's goal was to gather the power of all the Tailed Beasts in order to obtain great power and threaten the entire ninja world. They had carried out many missions, including destroying villages, kidnapping, and murder. Pei En was the founder of Akatsuki. He used the dark ninjutsu, the Eye of Darkness, to control the Nine-Tailed Fox and become a powerful ninja.
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.
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.
Pain would still be a likely candidate. His Rinnegan gives him a powerful and commanding presence. He has the ability to see the big picture and make strategic decisions for the group.
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One of the most popular female characters in Akatsuki in fanfictions is Konan. Her unique paper - based abilities and her complex relationship with Nagato and Yahiko make her a fascinating subject. In many fanfictions, her backstory is explored more deeply, especially her time growing up in the war - torn land of Amegakure. Another popular one could be Karin. Her connection to Sasuke and her own powers as a sensor type ninja give a lot of room for fanfiction writers to create interesting storylines, like her dealing with her feelings for Sasuke while being involved with the Akatsuki.
Pain would be one of the most challenging. His Rinnegan gives him a wide range of powerful abilities like the Six Paths of Pain. Naruto would have to figure out how to counter each of those paths and find a way to reach the real Pain. Itachi is also tough. His Sharingan and genjutsu skills are top - notch. Naruto would need to break free from his genjutsu and then find a way to fight back against his fire - based attacks.