A frequent plotline is that the mother uses her knowledge of the Uchiha to train Naruto in unique ways. This could include teaching him special jutsu or combat styles that are inspired by the Uchiha. In addition, there might be a plot where the mother's past relationships with the Uchiha clan members are gradually revealed as Naruto uncovers more about his own heritage in the fanfiction.
One common plotline could be the mother trying to hide Naruto's connection to the Uchiha from the rest of the village. Since the Uchiha had a somewhat controversial history in Konoha, she might be worried about Naruto being ostracized. Another plotline could be Naruto inheriting some sort of special Uchiha - related power from his mother, which he then has to discover and master as he grows up.
One common theme is power. Since Madara was extremely powerful, fanfictions often explore how Naruto deals with this new - found power if he is related to Madara. Another theme is identity. Naruto has to figure out who he is now that he has this connection to Madara Uchiha.
Often, in these types of fanfics, the 'bad mother' might be involved in some sort of betrayal. For example, she could be secretly working against the village or her own family in the Naruto context. It might also involve a mother who is self - centered and puts her own desires above her children's well - being. This can create a lot of conflict and drama within the fanfic, as it goes against the more positive family dynamics usually shown in the Naruto series.
One common plot element is the early access to the Sharingan. Since Naruto is born an Uchiha, he usually gets the Sharingan much earlier than in the original series. Another is the change in his relationships. His bond with Sasuke becomes different as they are now clan - mates. Also, he often has to deal with the Uchiha clan's secrets and history, which was a big part of Sasuke's story in the original but now becomes Naruto's too.
One common plotline is Naruto being betrayed first. He gets hurt so deeply that he turns against the world. For instance, if the Hidden Leaf Village, which he always considered his home, turns on him for some false accusations. This betrayal makes him snap and start seeking revenge, which in turn leads to him causing destruction all over the world.
A common plotline is Naruto being corrupted by the darkness. Maybe he's exposed to a powerful dark entity or power source that slowly starts to change his personality. For example, he might become more withdrawn and aggressive.
Often, there is a plotline about how Naruto's new bloodline affects his relationships. His friends may be in awe, some may be jealous, and his enemies will definitely be more interested in him. In some fanfictions, his new bloodline even causes rifts in his friendships at first as they struggle to understand this new side of him and the power he now wields.
Some fanfictions have Naruto uncovering dark secrets about Konoha. These secrets could be about the actions of the previous Hokages or the village elders. Discovering these secrets makes Naruto lose faith in Konoha and start to hate it.
One common plotline is the struggle for control. Naruto has to fight against the entity possessing him, like in many fanfictions where he battles his own body's takeover. Another is the reaction of his friends. They usually try to find a way to save Naruto, which often involves researching ancient texts or seeking out powerful ninja who might know a solution.
One possible plotline could be that Naruto's mother, being an Uchiha, passes on some unique Uchiha abilities to Naruto. Maybe he has an easier time learning certain jutsus related to the Sharingan, even without actually having the Sharingan himself. For example, he could have a natural affinity for fire - style jutsus which are common among the Uchiha.
In some fanfictions, the focus could be on Hermione's child's unique abilities or challenges. Since Hermione is very intelligent, her child might inherit her smarts but also have some special magical gift that she has to figure out how to handle on her own. Maybe the child has an uncontrollable power and Hermione has to search for ways to help the child manage it without a partner to support her. It could also involve her reconnecting with old friends from Hogwarts who either support or question her decisions as a single mother.