Perhaps he succumbs to an old wound or illness that has been haunting him throughout the story. In fanfiction, the author might play with the idea of his age finally catching up to him, and he dies a peaceful death in his sleep or while reminiscing about his life.
There's a possibility that it's one of his old enemies who has finally found a way to defeat him. Maybe they've discovered a weakness in Logan's healing factor or have a new weapon that can kill him. For example, if it's a foe who has studied him for a long time and found a way to disrupt his mutant abilities.
Another scenario could be that Iron Man is poisoned or infected with a deadly alien virus. He tries to fight it off but eventually succumbs to it. His friends in the Avengers try their best to save him but are unable to. This would be a really tragic way for him to go, especially considering how much he has done for the team and the world.
One possible scenario could be that Spider Man sacrifices himself to save the city from a powerful and unstoppable villain. He might use all his strength and powers to defeat the enemy, but in the process, his body gives out due to the extreme exertion.
In some fanfictions, Peter might die heroically while saving the city from a powerful villain like Venom. He could sacrifice himself to protect his loved ones and the innocent.
One possible scenario could be that Naruto was severely injured in a battle, perhaps against a powerful new enemy. He was brought to the hospital, but his injuries were too grave to be healed, and he passed away surrounded by his friends and family, leaving everyone in deep sorrow.
One possible scenario could be that Luffy sacrifices himself to save his crew during a major battle against an extremely powerful enemy. He might use all his strength and energy to protect them, and in the end, it's too much for his body to handle.
One possible scenario could be that Tony is in Siberia on a mission gone wrong. Maybe he's facing a powerful enemy there, and despite his best efforts, he gets fatally injured in a fight. Another could be that the harsh Siberian environment plays a role, like he gets caught in a blizzard and succumbs to the extreme cold.
One possible scenario could be that Percy sacrifices himself to save Annabeth from a powerful and deadly monster. Maybe a huge and ancient sea creature that only Percy can hold off long enough for Annabeth to escape, but at the cost of his own life.
Perhaps in the fanfiction, Naruto is betrayed during the battle. By someone he trusted, like a comrade who was secretly working for the enemy. This betrayal catches him off - guard, and he is severely injured. Unable to fully recover, he succumbs to his wounds during the fight.
Perhaps Naruto is betrayed by someone he trusts deeply. This person leads him into a trap at the Valley of the End. Naruto, being caught off - guard, is fatally wounded. His death in this fanfiction could be a tragic end to his journey of becoming a great ninja and a symbol of how even the most powerful can be brought down by treachery.