Well, perhaps in this 'naruto invasion of konoha fanfiction', Naruto is actually being mind - controlled to lead the invasion himself. It would be a huge shock for his friends and allies when they find out. This could lead to a lot of internal conflict as they try to figure out how to stop him without hurting him.
One possible plot twist could be that when they go back in time, they accidentally change something that has a huge impact on their future relationships. For example, Naruto might unknowingly prevent Sasuke from leaving the village in the past, which could completely change how they interact in the present they return to. Another could be that they find out a hidden truth about their parents or the village's past that was covered up, like a secret alliance that their predecessors were involved in.
A possible plot twist could be that sakura's real family from her non - Konoha origin has a secret connection to a major villain in the Naruto world. This would put her in a difficult position as she tries to balance her loyalty to her new friends in Konoha and her family ties.
A great plot twist might be that some of the villagers who were thought to be innocent are actually in cahoots with Pain. They could have been secretly helping him all along, providing information or weakening Konoha's defenses from the inside. This would shatter Naruto's perception of the village and add a lot of drama and conflict to the story as he has to deal with both external and internal enemies.
A possible plot twist could be that one of the Autobots is actually being controlled by an old enemy from Naruto's world. This enemy has found a way to hack into the Autobot's system and use it for their own revenge. So, while the Autobots seem to be helping Naruto, in reality, they might be leading him into a trap.
A possible plot twist could be that Naruto turns out to be a keyblade wielder in disguise. This would completely change the dynamic as everyone in the Naruto world and Kairi would be shocked. It could also mean that Naruto has a whole different origin and mission related to the world of Kingdom Hearts.
A possible plot twist could be that Naruto discovers he has a hidden connection to Smaug. Maybe he is related to Smaug in some long - lost magical way. Another twist could be that Smaug is not really a villain in this fanfiction. Instead, he is being controlled by a greater evil, and Naruto has to figure out how to free Smaug from this control. It would change the whole dynamic of their relationship from one of enmity to a more complex situation where they could potentially become allies.
A potential plot twist could be that Naruto's hatred is actually a cover - up for his love. He might be pretending to hate Konoha and his family to protect them from a greater threat. Maybe there's an enemy who would target them if Naruto showed any affection, so he creates this false front of hatred.
One common plot twist could be that Naruto is chased out due to a false accusation. For example, he might be wrongly blamed for a major crime in Konoha. Another could be that a powerful and secretive group within Konoha sees Naruto as a threat to their hidden plans and arranges for his expulsion. Also, it might be that Naruto discovers some dark secrets about Konoha's leadership and they try to silence him by chasing him out.
A possible plot twist is that Naruto leaves Konoha and enters a post - apocalyptic version of the ninja world. Resources are scarce, and different clans have formed alliances in unexpected ways. Naruto's ideals are put to the test as he tries to bring hope and unity in this desolate setting. He may have to make tough choices between old friends from Konoha and new comrades he meets in this new world.
One possible plot twist could be that they are being secretly manipulated by an unknown enemy who wants them out of Konoha for some dark purpose. Maybe this enemy has spread false rumors about them in the village, making them feel like they have no choice but to leave. Another plot twist might be that they discover a long - hidden truth about their families that is connected to some ancient power outside of Konoha, which compels them to leave in search of answers.