The story mainly revolves around Edgeworth's struggle to determine the meaning of his job in relation to finding the truth behind a collection of cases. This is exacerbated when he becomes a target of the so-called "Prosecutor Purge", an inquisition conducted by the Prosecutorial Investigation Committee intended to weed out and replace prosecutors who are judged to be incompetent or acting inappropriately.
Judge Hakari Mikagami is mysteriously sent to cases that Edgeworth is investigating and attempts to replace him with a younger, less competent prosecutor named Yumihiko Ichiyanagi. Edgeworth himself risks his badge in order to continue his quest for the truth.
In the meantime, he faces a personal conflict when he meets Tateyuki Shigaraki, a defense attorney who used to be an assistant to Edgeworth's father Gregory Edgeworth and has taken over the Edgeworth Law Offices after his death. Shigaraki offers the younger Edgeworth the chance to follow in his father's footsteps and become a defense attorney.