In this fanfiction, the Ministry could have been infiltrated by Voldemort's supporters even after his defeat. Harry realizes that the only way to truly end the threat and bring peace back to the wizarding world is to completely destroy the Ministry and rebuild it from scratch. So, he uses his knowledge of magic, his courage, and the loyalty of his friends to take on this huge task.
It could be that the Ministry has turned against the wizarding community in the fanfiction. Harry, being the hero, feels the need to destroy it to save his friends and the rest of the wizards. He might start by gathering evidence of their wrongdoings and then use his magic and the help of his friends to stage an attack on the Ministry's infrastructure.
Well, perhaps Harry discovers some dark secrets within the Ministry that are so evil he decides to take it down. Maybe they're involved in some sort of illegal dark magic experiments or corrupt deals with dark wizards.
Well, perhaps Harry has finally had enough of the Ministry's corruption and inefficiency. So he decides to take it down using his powerful magic skills. He might start by exposing all the dark secrets hidden within the Ministry walls, which could lead to chaos and the downfall of those in power.
It could be that there's a powerful enemy that has taken over Hogwarts and Harry, in a desperate attempt to stop this evil from spreading, resorts to destroying the school. He might think that rebuilding it later is better than allowing it to be used for evil purposes. For example, if Voldemort had found a way to permanently taint the magic of Hogwarts, Harry might see destruction as the only option.
The Order of the Phoenix members might also back Harry. They've fought against the dark forces before and if they see that the Ministry has become a threat, they'd side with Harry. Dumbledore's old allies in the Order would believe in Harry's judgment and join him in his mission to destroy the corrupt Ministry.
In this fanfiction, it could be that a new law is passed in the wizarding world. The law states that anyone with the ability to defeat a dark lord must be executed to prevent them from becoming a dictator in the future. Harry, being the only one known to have defeated Voldemort, is targeted by the Ministry. He has to rely on his old Hogwarts allies and some unexpected new friends within the Ministry to fight this unjust law and save his own life.
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.
One possibility could be that Harry discovers some dark magic or a hidden conspiracy within the Triwizard Tournament that forces him to take extreme measures and destroy it. Maybe he finds out that the tournament is being used as a cover for an evil plot against Hogwarts or the wizarding world in general.
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.
A possible plot could be that Susan Bones gets a job at the Ministry right after graduating from Hogwarts. She notices some strange activities going on that seem to be related to the return of dark magic. She then reaches out to Harry Potter for help as she believes he has the experience to deal with such things. Together, they start an investigation within the Ministry to uncover the truth.
Ron and Hermione are almost surely his allies. They've always been by his side through thick and thin. Hermione's vast knowledge of magic and Ron's loyalty and courage would be invaluable in a mission to destroy the Ministry.
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.