The toads themselves would be majorly affected. Since Naruto died while trying to summon them, they would carry the burden of his death. His friends in the village like Shikamaru, who often strategized with Naruto, would also be hit hard. They would have to adjust to a world without Naruto's unique perspective and power. And then there's Hinata, who had feelings for Naruto. His death would be a crushing blow to her.
Sasuke would definitely be one of the main characters affected. He and Naruto had a complex relationship, and Naruto's death would likely trigger a range of emotions in Sasuke, from grief to anger. Sakura too, as she cared deeply for Naruto. Also, Kakashi, who was Naruto's teacher, would be deeply affected. He had seen Naruto grow and would feel a great sense of loss.
The Hokage at that time, whether it was Tsunade or someone else, would be affected. Naruto was seen as a future hope for the village. His death could make the Hokage question their leadership and the safety of the village. The other ninja clans in the village would also be affected as Naruto was a unifying figure among them. They would have to reevaluate their relationships and future plans without Naruto.
His death would be a huge turning point. It could lead to the dissolution of some alliances that were centered around Naruto. For example, the toads might feel a sense of guilt since he died trying to summon them. This could make them withdraw from the affairs of the ninja world. On the other hand, villains could become bolder, seeing the absence of Naruto as an opportunity to take over. It would be a very dark turn for the plot.
In addition to Sasuke, Kakashi, and Sakura, other characters like Iruka sensei would be affected. Iruka was one of the first people to believe in Naruto. Naruto's death would be a huge blow to him. Also, the villagers of Konoha who had started to see Naruto in a new light might have to re - evaluate their views. And characters in the Land of Waves, like Tazuna and his family, who had come to rely on Naruto's help, would also be impacted. They might lose hope or face greater danger without Naruto there to protect them.
The main character is Naruto without a doubt. His journey of becoming godlike is the focus. The toads are also main characters. Big - name toads such as Fukasaku and Shima could be in it. They are likely to be the ones teaching Naruto. Their guidance and the bond between Naruto and the toads are important aspects of the story, making them all main characters in this fanfic.
Twilight Sparkle would definitely be one of the main characters affected. As Spike was her assistant and friend, his death would leave a huge void in her life.
The villagers themselves could be responsible. Their constant ostracization and negative treatment of Naruto could lead to his downfall. He might be pushed to a point where he takes risks that ultimately cost him his life.
Often, Naruto himself can be a main character. He might be the one who either accidentally or intentionally summons the pony. Another common main character could be the pony that is summoned, which has its own unique personality and abilities.
Since I haven't read it, I can't say for sure. But it could be Naruto, as he is the main character of the original series and has a lot of pain in his past. It might also focus on Sasuke, who has his own set of traumas and pain related to his family and his quest for revenge.
If Emily is related to Marinette, Marinette would surely be one of the main characters affected. She might feel guilty, especially if she could have done something to prevent Emily's death. Marinette could also become more determined to fight against evil in Emily's memory.
Definitely Naruto. His identity as a jinchuriki has defined so much of his journey. Without the Nine - Tailed Fox, he has to redefine himself. Hinata too could be affected. She has always admired Naruto, and his change in power status could change their relationship dynamics. Then there's Tsunade. As the Hokage, she has to deal with the political and military implications of Konoha losing the power of the Nine - Tailed Fox. Konoha as a whole is also a main 'character' in a sense. The village has to adapt to the new situation where the powerful Nine - Tailed Fox is no longer there to protect or threaten it.
In addition to Naruto and Sasuke, characters like Kakashi could also be main characters. He is a very popular character in the Naruto series, and his wisdom and combat skills could be crucial in a story involving the 'death god'. Also, characters like Sakura might be there. She could be involved in the story either as a healer or as someone who also has to deal with the new and dangerous elements brought by the 'death god' concept.