Naruhodo Ryuichi (Phoenix Wright), attorney at law, sets foot in a courtroom for his very first trial... in which he has to defend his best friend?!

Phoenix suffers a blow to the head from behind and loses his memory right before a trial, in which he is defending police officer Maggey Byrde for the murder of her boyfriend and fellow officer Dustin Prince.

Five years ago, Phoenix is accused for the murder of Doug Swallow, who was electrocuted to death. Mia, who had previously been traumatized by her first trial a year ago, defends Phoenix in court, where Payne suggests Phoenix had bad blood with Swallow over his then girlfriend Dahlia Hawthorne and pushed him into a severed electrical cable.

Phoenix, Maya, and Pearl go to Hazakura Temple for Maya's training, where they meet children's book author Elise Deauxnim and nuns Bikini and Iris, along with Larry, who is studying as Elise's apprentice.

Noticing that Maya was able to identify the true culprit in the dark, Phoenix deduces that the killer is Godot, whose red visor not only glows in the dark but also leaves him unable to see anything red, including the bloody message incriminating Maya.