Another scenario could be that they are poisoned by a new, undetectable toxin. As they gradually weaken, they try to find a cure but run out of time. Their deaths would be a great loss, and it could lead to major changes in the political and social structure of the ninja world as everyone copes with their passing.
One possible scenario could be that they sacrifice themselves to save the village from an ultimate evil. They might combine their powers in a final, desperate move that exhausts them completely, leading to their deaths.
One possible scenario could be a power imbalance. Maybe Sasuke discovers some new, extremely powerful jutsu that Naruto has no defense against. For example, a jutsu that can nullify Naruto's chakra or attack his spirit directly. Another possibility is a miscommunication or a breakdown in their relationship. If Sasuke believes Naruto has betrayed him in some way, his anger could lead him to kill Naruto. However, this goes against the core of their bond in the original series.
Another scenario could be that Naruto and Sasuke discover a new power within themselves during the fight against Kaguya. This new power could be related to their friendship or their connection to the Sage of Six Paths. They then use this power to finally defeat Kaguya.
Well, in some versions of this fanfiction, it might be that Naruto uses a powerful and forbidden jutsu to defeat an overwhelming foe. This jutsu drains his life force, and Sasuke, who has just realized how much Naruto means to him, catches Naruto as he collapses. It could also be that Naruto is poisoned, and Sasuke tries his best to save him but fails in the end, and Naruto passes away in his arms.
In some fanfictions, Naruto might jump in front of Sasuke during an emotional moment. For example, if Sasuke is about to make a rash decision that could put his life in danger, Naruto jumps in front to stop him and talk some sense into him. Naruto's presence in front of Sasuke could also symbolize his unwavering loyalty and friendship towards Sasuke, showing that he'll always be there for him no matter what.
Perhaps Naruto has some sort of premonition about Sasuke's danger. He follows his gut feeling and finds Sasuke trapped by Haku. He then uses his Uzumaki bloodline power, something that might be enhanced in fanfiction, to disrupt Haku's chakra flow and save Sasuke.
Maybe in a moment of reconciliation. After years of being apart and having misunderstandings, when they finally come back together and forgive each other, the emotions are so strong that a kiss just happens. It could be a very emotional and slow - building moment, with lots of words of apology and understanding first.
One possible scenario is that Naruto loses all his powers. He has been defined by his strength and his ability to protect. Without it, he may feel useless and worthless, leading to a desire to die. For instance, if he is cursed and loses his chakra completely.
One possible scenario could be that Naruto snaps at Sasuke over his constant pursuit of power at the expense of their friendship. Maybe Sasuke makes a decision to leave the village again for more power, and Naruto, tired of his friend's self - destructive ways, snaps and tries to make him see reason.
One interesting scenario could be a fight in an alternate dimension where the rules of chakra are different. This would force both Naruto and Sasuke to adapt new strategies. Another could be a battle where they are forced to team up against a common enemy first before their duel, which would add a complex layer of emotions and dynamics.