Perhaps an ancient evil that has been awakened. This could be a powerful demon or a spirit that was sealed away long ago. It targets Naruto because of his own status as a Jinchuriki. It wants to use Naruto's power for its own purposes, and when Naruto resists, it kills him. The ancient evil could have powers that are completely beyond the understanding of the ninja world at that time.
A rogue ninja from another village could be the main antagonist. Maybe a ninja from the Hidden Mist Village who has a personal grudge against Konoha and sees Naruto as the symbol of Konoha's strength. So, he devises a complex plan to take down Naruto. This ninja could have some unique and deadly jutsu that Naruto has never faced before, which ultimately leads to his downfall.
A new organization that is bent on world domination could be the main antagonist. They set a trap during Naruto's mission. This organization might have access to some ancient and forbidden jutsu that they use against Naruto. They see Naruto as a major threat to their plans, so they target him specifically.
It could be a rogue ninja who was secretly plotting against Naruto all along. After Naruto's death, this antagonist could emerge and try to take over the village, seeing it as the perfect opportunity with the village in mourning and a bit disorganized. This ninja might have some personal vendetta against Naruto and now wants to make the village pay.
It could be a powerful sorcerer who wants to take over Crookshnks' homeland. This sorcerer has dark magic and sees Crookshnks as a threat to his plans, so he devises a scheme to eliminate him.
It could be a new character created just for the fanfiction. Maybe a rogue ninja who has mastered a dark and powerful jutsu that Naruto has no defense against. This antagonist could be seeking revenge on Konoha for some past wrong and sees Naruto as the biggest threat to his plans.
It could be someone who was secretly behind Naruto's death in the first place. Maybe a rogue ninja who has a vendetta against the Hidden Leaf and saw Naruto as a major obstacle.
It could be an ancient evil that was sealed away long ago but has been released due to Naruto's death. Maybe Naruto's sacrifice in his previous life weakened the seal, and now this evil has emerged. It could be a powerful demon or a dark ninja with extremely strong and malevolent jutsu.
It could be Orochimaru. Since Naruto was a potential threat to his plans in the original story, if Naruto died as a baby, Orochimaru might be able to carry out his experiments and schemes more freely without having to worry about Naruto interfering in the future.
It could be an unknown shinobi from a far - off land. A shinobi with powers that Naruto has never encountered before. This new antagonist might have some dark and powerful jutsu that Naruto simply isn't prepared for, which ultimately leads to his downfall on the bridge.
An alien race with a grudge against the Republic could also be the main antagonist. They might target Rex specifically because of his strategic importance and his role in leading many successful missions against them in the past. His death at their hands would be a major blow to the Republic's morale.
It could be a rival family who had some sort of long - standing feud with Sakura's family. They might have caused their deaths in an underhanded way and now Sakura has to deal with them as she tries to uncover the truth.