One possibility could be that Naruto has been poisoned by a new and unknown enemy. This poison is slowly eating away at his life force, and he's trying to hide it from his friends and family so as not to worry them. He might be secretly seeking a cure while still fulfilling his duties as Hokage.
In this fanfiction, it could be that Naruto's overuse of the Nine - Tails' power has led to some unforeseen consequences. The chakra of the Nine - Tails might be slowly corrupting his body from the inside out. He's keeping it a secret because he doesn't want to lose the trust of the village that has come to rely on his power. He's secretly looking for a way to reverse the damage while still being the strong leader everyone expects him to be.
Maybe there's a curse placed on Naruto that is causing him to die secretly. It could be related to some old, forgotten shinobi magic. In the fanfiction, the curse could be slowly draining his chakra and his very essence. He'd be struggling to keep up his normal appearance while he desperately tries to find a way to break the curse.
It could be a rogue shinobi from Naruto's past who has been biding his time. This shinobi might have developed a new jutsu specifically designed to target Naruto and make him die slowly. He's doing it secretly to cause chaos in the Hidden Leaf when their hero suddenly passes away.
Maybe Naruto has always idolized the Hokage in secret. He could be studying the ways of past Hokages on his own, trying to learn their leadership skills and jutsu. For example, he might be secretly practicing Minato's Flying Thunder God Technique because he admires his father so much.
One possible plot could be that Naruto faked his death to go undercover in a powerful and evil organization. He pretends to be a new recruit while secretly gathering information to take the organization down from the inside.
One possible plot could be that they are secretly working together to stop a new threat in the ninja world that no one else is aware of. Itachi's intelligence and Naruto's determination would make a great team. They might be gathering information in the shadows, using Itachi's skills in espionage and Naruto's ability to make connections with different ninja clans.
Perhaps in the fanfiction, there is a common threat to both of their villages. Naruto and Mei work together closely to fight against this threat. During this time, they develop feelings for each other. They secretly marry to show their commitment to each other privately. But then they face difficulties like spies from other villages suspecting their relationship and trying to use it against them, and they have to outwit those spies.
Well, perhaps in this fanfiction, Naruto discovers his talent for brewing by accident. He might start by brewing simple herbal teas at first, but as he gets more into it, he begins to create complex concoctions. His brewing could be related to his chakra control, like he discovers a way to infuse chakra into his brews for extra effects. He'd have to keep it secret because it's a new and untested ability in the ninja world.
One possible plot could be that they got married in a secret ceremony for political reasons. Maybe to strengthen an alliance between their villages. They then have to keep their relationship a secret while still dealing with the daily challenges in their respective villages.
One possible plot could be that Naruto, feeling neglected by the village in some way, starts to idolize the Anbu. He might secretly train in the ways of the Anbu, observing them from afar. Maybe he discovers a conspiracy within the Anbu and has to decide whether to expose it or help fix it on his own while still being an outsider to the group.
A possible plot twist is that Naruto is actually a reincarnation of a great Jedi. He starts having strange dreams and visions of a past life as a Jedi, and these memories gradually influence his actions as a ninja. His friends might be confused or even a bit scared at first, but as he learns to control this new side of himself, they come to accept and rely on his Jedi - inspired skills in their battles against stronger foes.
I'm not sure specifically as there could be many different interpretations. It might be about a character named Sakura who is secretly in a deteriorating state, perhaps physically ill or emotionally broken in the context of the fan - made fictional story.