One possible plot could be that Thor arrives in Konoha and is initially mistaken for a powerful new enemy. The shinobi of Konoha are on high alert. But as they soon realize he has no ill intent, Thor starts to learn about the chakra system. He might even share some of his Asgardian knowledge about magic and combat with the ninja. For example, he could teach them new ways of using their physical strength in battle.
Naruto would be a likely ally. Naruto is always open to making new friends and with his strong sense of justice, he would see Thor as someone who can help protect Konoha. Another potential ally could be Kakashi. Kakashi is a very experienced and intelligent ninja. He would be able to quickly assess Thor's abilities and find ways to work together effectively.
In such a fanfiction, Goku might be seen as a very powerful and strange visitor in Konoha. He could start by showing off his amazing strength and speed during a training session with the ninja. Maybe he'd accidentally break some training equipment and leave everyone in awe.
It could be Iruka. Since Iruka is an important teacher in Konoha, he might be the first to notice Goku's arrival. He'd probably be cautious at first, not knowing what to make of this powerful being, but then try to figure out if Goku is a threat or not.
In a fanfiction scenario, Naruto could bring his ninja skills to the modern Konoha and start a new trend. Maybe he'd teach the modern-day shinobi some of the old - fashioned but effective ninja techniques. Also, he'd be amazed by the new training facilities and the different ways of life. He might struggle with the concept of modern education though, as he was used to the more hands - on ninja training.
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.
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 popular theme is the daily life in Konoha. It could be about the characters going about their normal days, training, having fun at the local shops, or just hanging out with friends. Another theme is about Konoha during a war or a major threat. How the village prepares, the strategies they come up with, and how the characters, especially Naruto, contribute to the defense. And then there's the theme of Konoha's past. Stories that explore the history of the village, the founders, and how things have changed over time.
They could bring new ideas. For example, if they come from a different place, their cultural ideas might influence Konoha's fashion or food. Their presence might also inspire the local kids to work harder in their ninja training, seeing two new and exciting role models.
It would be a huge blow to Konoha. Naruto is a hero in the village, and his departure would leave a big leadership void. The villagers would also lose a great source of inspiration. Hinata is from a respected clan, and her leaving would also have an impact on the clan's standing in the village. Morale among the ninjas might drop as they see two important figures leave.