Perhaps a plot where Naruto is framed by an unknown enemy who has the ability to manipulate the minds of the villagers. As a result, the villagers turn against him and he has no choice but to flee. Along the way, he might meet new characters or develop new powers as he tries to figure out who is behind this and how to reverse the situation.
In some 'naruto flee on sight fanfiction', there might be a plot where Naruto discovers a dark secret about the village elders and they try to silence him, making him flee. This could involve him uncovering some unethical experiments or power - hungry plans that the elders don't want to be made public. So he has to escape their clutches and find allies outside the village to expose the truth.
One possible interesting plot could be Naruto being forced to flee due to a false accusation within the Hidden Leaf Village. Maybe he's wrongly suspected of a crime and has to run while trying to clear his name.