Maybe Harry Potter decides to sue the Ministry because they have been withholding important information about his family or his true destiny. It could also be that the Ministry has been unjustly persecuting him or his friends, and he decides to take legal action within the wizarding world's framework.
Hermione could be a key character. She is always by Harry's side, and her intelligence and knowledge of the wizarding laws would be invaluable in the lawsuit. She might be the one doing all the research and preparing the legal arguments for Harry.
Maybe Harry Potter sues the Ministry for false accusations or for not taking proper actions against dark forces. It could also be about some new laws the Ministry made that directly harm Harry or his friends.
In this fanfic, Harry could be suing the Ministry over their education policies. For example, Hogwarts might be facing some unfair regulations that are harming the students' learning experience. Harry, having a strong sense of justice, takes on the Ministry. He might gather support from other students, teachers, and even some of the wizarding families who are also affected by these policies. He would then present his case in a wizarding court, which could be full of all sorts of magical procedures and challenges.
Hermione would most likely be one of his top allies. She's smart and well - read in wizarding law, so she could help Harry build his case. Ron would also be there for moral support and to offer his own unique perspective on things.
Perhaps he uncovers some major corruption or inefficiency in the Ministry. So, as a result of his efforts to reform it, he is given control. For example, if he finds that the Ministry has been misusing magic for personal gains, he could lead a movement to take it over and run it in a more just way.
He might openly oppose their policies. For example, if the Ministry tries to pass a law that restricts the use of certain spells for self - defense, Harry could publicly speak out against it, giving interviews or writing articles in wizarding newspapers.
One possible reason could be the Ministry's corruption. In the original series, the Ministry often showed signs of being influenced by dark forces or being overly bureaucratic and not seeing the real threats. So in the fanfiction, this might be a driving factor for Harry to oppose them.
Well, in some fanfictions, Harry Potter might come to own the Ministry of Magic through his heroic deeds. He could have defeated a great evil that threatened the wizarding world so severely that the wizarding community decides he is the most fit to take over and reform the Ministry.