Another scenario could be in a mission gone wrong. The fanfiction might depict a mission where Naruto and his team are caught off - guard by an ambush. There could be a large number of well - coordinated enemies, and Naruto might end up being the main target, getting severely injured as he tries to fight them off and protect his team.
A new and powerful rogue ninja could be responsible. This ninja might have a vendetta against Konoha and see Naruto as a symbol of the village, so they target him and use their strong and devious techniques to injure him badly.
The Hokage at the time, whether it's Tsunade or someone else, would likely get involved. They would allocate resources and ensure that the best medical care is provided. Additionally, some of the older ninja who knew Kakashi since he was young, like Iruka, might offer moral support and assist in any way they can, like gathering information or running errands related to his treatment.
One possible fanfiction could be that Naruto is transported to the Fairy Tail world through some magical anomaly. In a battle against a powerful dark mage in Fairy Tail, Naruto, not fully understanding the magic system there, gets badly injured. He has to rely on the kindness of the Fairy Tail guild members to heal and learn about their magic to get back on his feet.
It might be that he was trying to protect some of the Fairy Tail guild members from a dangerous enemy. In the process, he took on more damage than he could handle. For example, if a powerful demon was attacking the guild, Naruto might jump in front of it to save his newfound friends, getting seriously injured in the process.