Naruto could outsmart Konoha by leveraging his relationships. He has friends all over the village, and he might use their skills and loyalty in a clever way. Maybe he arranges for a coordinated effort among his friends to expose a plot within Konoha that others are oblivious to, thus showing his superior intelligence in handling the situation.
Well, in some fanfictions, Naruto might outsmart Konoha by using his unique knowledge of the village's secrets that others don't know. For example, he could use his understanding of the old tunnels under Konoha to his advantage in a situation where he needs to escape or gain an upper hand in a conflict.
One key plot point could be Naruto discovering a conspiracy within Konoha. He then uses his wits to gather evidence without being detected. Another might be when he outmaneuvers the village elders in a political situation, perhaps by using the support of the younger generation.
Konoha would initially be in shock. Naruto is a hero to many in the village, and his sudden departure with Itachi, who was once considered a traitor, would cause a lot of unrest. The villagers might start to question the leadership of the village, wondering why Naruto left and if there was something they could have done to prevent it.
In some fanfictions, Konoha may suffer due to powerful villains specifically targeting it. For example, a new and extremely strong dark ninja group could launch a surprise attack on Konoha, causing destruction and loss of lives among its shinobi. This could also lead to a breakdown in the village's infrastructure and a sense of fear and despair among the villagers.
Well, it would be a big loss for Konoha. Naruto is a powerful ninja, and his absence would mean one less strong fighter to defend the village. Ino, too, has her unique skills in mind - related jutsu and communication. Their departure might also lower the morale of other ninja, especially those who were friends with them or looked up to them.
Konoha might be in shock at first. They have always relied on Naruto to some extent, and his refusal to help is completely unexpected.
He would probably be very angry. Naruto has always been a free - spirited person, and being experimented on against his will would be a huge violation of his rights. He might initially try to resist physically, but as the situation gets more complex, he could start to plot his escape and revenge.
At first, Naruto is likely to be heartbroken. Konoha has been his home, and he has always longed for acceptance from the villagers. So being abandoned would be a huge blow to him.
It could lead to political unrest in Konoha. There might be those who blame the village leadership for Naruto's departure. This could lead to power struggles as different factions try to take control and change the way the village is run. Some might demand more transparency and better treatment of their shinobi to prevent such a thing from happening again.
It could create a sense of unease and fear. Naruto is a very powerful ninja, and if he turns dark and leaves, the villagers would be worried about him coming back as an enemy. It might also lead to a decrease in morale among the ninjas who once considered Naruto a friend or ally.
Maybe he feels betrayed. In the original story, Naruto has faced a lot of discrimination in Konoha when he was young. So in the fanfiction, it could be that some similar or new issues make him decide to hide.