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Because he still wanted to side with the ministry. Even if the ministry believed that Voldemort was back, they still didn't like the Order of the Phoenix, Dumbledore, or the Weasleys. Percy wanted to climb the power ladder and disengage himself from his father who worked in a low position there. He came around during the Battle of Hogwarts, though. He told his family that he had been trying to figure out how to leave for a while. But traitors were being arrest. He had made contact with Aberforth. When the battle was about to start, Aberforth told him about it and he joined them.