Perhaps in the fanfiction, there's an alternate universe scenario where Harry has a different personality. He might be more power - hungry and sees his family as obstacles to achieving greater power, so he takes actions to get rid of them. This could involve using his magic in cruel and calculated ways against his family members.
Another idea could be that Naruto discovers some dark family secrets that he can't bear. This could include things like his family being involved in unethical experiments in the past. The shock and disappointment are so great that he loses control and ends up causing harm to his family, though it's a very tragic and complex situation.
One possible plot could be that Harry discovers a dark secret about the Ministry of Magic, like they are using dark magic themselves to control the wizarding population. So he decides to expose them and in the process, the chaos that ensues leads to the destruction of magical Britain as it was known.
One possible plot could be that Naruto is somehow mind - controlled by a powerful enemy who forces him to turn on Konoha. Maybe the enemy has a special jutsu that can manipulate Naruto's emotions and memories, making him believe that Konoha has wronged him in some way.
Another possibility is that there could be a new character introduced in the fanfiction, a mastermind who manipulates Harry into believing that his family is a threat. This new character could be the main antagonist.
One possible reason could be a dark turn in the story. Maybe Harry is under the influence of a dark magic or a powerful and evil entity that makes him lose control and start to destroy Hogwarts. For example, if he was possessed by a powerful dark spirit that wanted to eradicate the symbol of the wizarding world's good, which is Hogwarts.
Well, one possible plot could be that Harry's love is taken away due to some dark magic. Maybe an enemy casts a spell that makes his love forget about him. Another could be that Harry has to sacrifice his love for the greater good, like to save the wizarding world. And also, it might be that there's a misunderstanding between them that causes the loss of love.
In such a fanfiction, perhaps Harry discovers some dark secret of Snape's that makes him decide to take action against him. Maybe Snape has been plotting something truly evil all along, and Harry finally uncovers it and has to destroy Snape to protect Hogwarts and his friends.
A possible plot could be centered around Tonks' pregnancy. In fanfiction, it could be explored how she coped with the difficulties during that time, especially considering the dangerous situation in the wizarding world. And how her family supported her.
One possible plot could be that they discover they are not actually related in a way that was previously thought. Maybe there was a big misunderstanding about their family relations all along. Another could be a story set in an alternate universe where the social norms are different and such a union is somehow acceptable within that fictional world's rules.
One interesting plot could be Harry's family going on a magical adventure together to a hidden wizarding land that no one has ever explored. They might encounter new magical creatures and solve mysteries there.