It could be Hinata. Even though in the original story they are openly married, in a fanfic scenario, there could be a situation where their relationship was kept secret for some time and she gave birth to a son secretly. Maybe due to some threat to the village or Naruto's safety.
Well, one plot twist could be that the son has some unique power that neither Naruto nor his friends are aware of at first. Maybe it's a power that was dormant until a certain event triggered it.
In most official Naruto lore, Naruto has no relation to Tsunade in that way. However, in fanfic, anything can be possible. It depends on the specific plot and creative ideas of the author of that particular fanfic.
I'm not sure which specific 'naruto is secret son of mito' fanfic is highly recommended. There are so many fanfics out there. You could try searching on fanfic - specific websites like FanFiction.net or Archive of Our Own and look at the reviews and ratings to find a good one.
In many fanfictions, Sakura could be a potential mother. Since she has a close relationship with Naruto in the original series, some fans might imagine a scenario where they end up together and have a son. Another possibility could be Hinata. Given her deep love for Naruto, it's not hard to fathom a fanfiction where they have a secret son.
His son could inherit Naruto's powerful chakra and the ability to use the Rasengan. Maybe also have some form of enhanced speed and strength like Naruto. After all, Naruto's powers are quite dominant.
A plotline could involve Naruto's identity being gradually revealed. There could be a lot of shock and disbelief among the villagers. Some might fear his power, thinking he has some hidden agenda as Mito's son. Meanwhile, Naruto would have to deal with his new - found identity and the expectations that come with it. He might also start to explore his connection to the Uzumaki clan more deeply and try to uncover secrets about his mother that were previously hidden. This could lead to all sorts of adventures and conflicts within the Naruto universe.
One implication could be a change in Naruto's social status within the village. He might be treated differently, perhaps with more respect due to Tsunade's position. Also, his training could have been different, as Tsunade might have imparted her own skills and knowledge to him earlier.
If Naruto was the secret son of Kushina and Mito in fanfic, one possible plot could be that Naruto inherits some of Mito's unique abilities related to the Nine - Tails. This could give him an even stronger connection to the Tailed Beast and new powers to discover. Another aspect could be a change in his relationships with other characters. For example, the Uzumaki clan might view him differently, and there could be a whole new set of political or family - related storylines.