Well, it could be that Naruto, using his ninja skills and knowledge, takes over the criminal underworld to reform it. Maybe he uses his powerful jutsus to intimidate the bad guys into following his new rules.
Perhaps Naruto enters the criminal underworld to find a particular villain or to stop a major threat that is being planned from within that world. Once there, he has no choice but to take over in order to gain control and put an end to the chaos. He would use his unique abilities like his shadow clones to keep an eye on different parts of the underworld, and his Rasengan to deal with any who oppose him too strongly.
Shikamaru could also be an ally. His intelligence would be invaluable in planning strategies and outwitting the more cunning criminals. He could help Naruto figure out the complex power structures within the underworld and come up with plans to either take them down or use them to Naruto's advantage.
In this fanfiction, Naruto could also face challenges in running the clinic. He might struggle with administrative tasks since he's used to the action - packed ninja life. But he could hire some of his ninja friends to help, like Sakura as a medical expert and Rock Lee to handle the physical tasks around the clinic.
In a 'naruto runs a shop' fanfiction, he could run a pet shop. Naruto has always had a connection with animals. He rescues and rehabilitates injured animals and then finds them new homes through his shop. He might also have some special ninja - animal hybrids in his shop that are a big draw for customers.
In this fanfiction, Naruto might run away to Iwa because he feels misunderstood in Konoha. Maybe he discovers some secrets related to his family that make him think Iwa has the answers. He could face many challenges on his way there, like avoiding capture by Konoha ninjas who think he's a traitor.
One possible plot could be that Naruto and Sasuke run away to find a place where they can train without the interference of the Hidden Villages. They might be on a quest to become stronger together, away from the prying eyes of their respective villages which have different expectations of them.
It could be that a prophecy or a false accusation is made against Naruto, saying he will bring destruction to the village. Hinata doesn't believe it for a second. Instead of waiting for the village to turn on Naruto, she convinces him to run away with her. They then travel to other villages, learning different jutsu and cultures, all while trying to clear Naruto's name.
One possible plot could be that Naruto runs away to Suna to escape some sort of danger in Konoha. Maybe there's a powerful enemy after him and he thinks Suna can offer him protection. He could also be running away from some internal conflict within Konoha, like issues with the villagers not fully accepting him still.
In this fanfiction, Naruto might leave the underworld because he has a mission to fulfill in the real world. Maybe he has to stop a new threat that endangers both the living and the underworld.
In a 'naruto runs away fanfic', one possible plot could be that Naruto runs away after feeling misunderstood by the village. He might go on a journey to find a place where he can truly belong. Along the way, he could meet new allies or enemies. For example, he might encounter a group of outcasts who are also on the run from different villages. They could team up and form a sort of 'runaway family' where Naruto learns new skills and perspectives outside of the Hidden Leaf's teachings.
Well, one possibility is that Naruto uses his own experiences as an orphan to create a warm and supportive environment in the orphanage. He might teach the kids ninjutsu skills and also important life lessons about friendship and perseverance.