In the Naruto series, Naruto doesn't have a biological sister in the original story. So in this fanfiction, the author probably creates a new character to be his sister. It could be an original character with unique abilities and a complex backstory that leads to the situation where Naruto dies by her hand.
There's a good chance he would meet Itachi. Itachi had a complex relationship with Naruto and played an important role in the overall story. In heaven, they could clear up any misunderstandings and Itachi could explain his actions more fully to Naruto, and Naruto could perhaps offer his forgiveness and understanding.
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.
He could interact with his old sensei, Iruka. Iruka was an important figure in Naruto's life, and as a ghost, Naruto might visit Iruka to give him some comfort or to seek advice. Since Iruka was always there for Naruto when he was alive, their connection could still exist in the afterlife.
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.
It could be an unknown, ancient evil that has been awakened. This villain might have powers far beyond what Naruto and Sasuke have faced before. Maybe it's an entity from a forgotten era that was sealed away long ago and now has broken free.
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 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.
Well, Kabuto can be a major antagonist in such fanfictions. Since he has a vast knowledge of jutsu and was once allied with Orochimaru, he could be the one causing Naruto to almost die. He might use his medical ninjutsu knowledge to create some sort of deadly virus or poison that specifically targets Naruto's unique chakra system. Additionally, Pain is also a common one. His Rinnegan abilities give him the power to cause a great deal of destruction. In fanfictions, he could be more ruthless in his attacks on Naruto, getting him to the brink of death.