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?!

With the DL-6 Incident and the lunch money case now solved, memories of fifteen years ago come flooding back.

During a Hero of Heroes Grand Prix event held at a hotel, one of the actors, Juan Corrida, is murdered, with the current Nickel Samurai actor, Matt Engarde, accused of the crime. Just after learning about the murder, Phoenix is contacted by someone known as Shelly de Killer, who reveals he has kidnapped Maya and will only release her if Phoenix can get Engarde acquitted within the trial's first day. The next day, Phoenix interviews Engarde's manager, Adrian Andrews, and investigates Corrida's dressing room. Just before the trial the following day, Franziska is suddenly shot by a sniper hired by de Killer, prompting Edgeworth, who has returned from his long absence, to take her place on the prosecutor's bench.

At the start of the trial, Gumshoe explains that, despite the obvious knife wound on the body, Corrida was actually killed by strangulation. Oldbag, who had been working security at the hotel, then testifies that she saw Engarde leave Corrida's room, presenting a photo of the Nickel Samurai costume. Noticing that the person in the costume is shorter than Engarde, Phoenix accuses Adrian and calls her to the stand. She reveals that she had planned to hold a conference with Corrida in the Nickel Samurai costume, as he knew a secret about Engarde's career. With Adrian refusing to testify and a lack of evidence to convict her, Phoenix is unable to stop the trial from becoming extended. After Phoenix manages to convince de Killer to give him more time, Edgeworth, learning about Maya's kidnapping from Phoenix, deduces from a calling card Adrian had picked up from the scene that Corrida was killed by de Killer, suspecting Engarde was the one who contracted him. Meanwhile, Maya manages to briefly break out of the basement and find a framed photo of someone before de Killer catches her again. Inspecting the crime scene again, Phoenix and Edgeworth discover a hidden camera hidden in one of the teddy bears, discovering Engarde was the one sent it. When confronted about it, Engarde reveals to Phoenix that he is indeed the one who contracted de Killer to kill Corrida.

Revealing that he hid the camera as insurance against de Killer, Engarde reminds Phoenix about what will happen to Maya if he fails to secure a "not guilty" verdict. As Edgeworth asks Phoenix to think about what the right thing to do is, they hear the sound of Engarde's pet cat over de Killer's radio, leading them to Engarde's mansion. Although Maya is nowhere to be found by the time they get there, they discover a photo of Adrian's sister, Celeste, and a message from Maya telling Phoenix to find Engarde guilty no matter the cost. The next day, as Edgeworth brings in Adrian to testify about a teddy bear that was removed from the crime scene, Pearl manages to use Mia to inform Gumshoe about Maya's current whereabouts. Adrian explains that the bear was a gift to Corrida from Celeste, who hung herself after being dumped by Corrida after he learned about her relationship with Engarde. She further reveals that Corrida was planning to reveal Celeste's suicide note to the public during the conference, leading Adrian to tamper with the crime scene in order to implicate Engarde. As the note is revealed to be inside the bear that was taken from the scene, Phoenix calls for the note to be analyzed to buy some time. Gumshoe manages to find some evidence left behind by Maya, but ends up getting into a traffic accident en route to the courtroom, where de Killer decides to testify over a transceiver.

De Killer claims that Adrian is his client, but exposes his lie when he wrongly assumes her to be a man. Just as de Killer adjusts his testimony and Engarde is about to be declared innocent, Franziska arrives with the video disk Gumshoe had picked up, containing footage of de Killer killing Corrida. Turning his thinking around, Phoenix shows the video to de Killer, revealing that Engarde had been planning to use it to blackmail him. Realizing he has been betrayed, de Killer cancels his contract with Engarde, choosing him as his next target, and releases Maya. Terrified for his own safety, Engarde is forced to confess his guilt. After the trial, as Franziska is baffled over Phoenix being happy with a guilty verdict, Edgeworth states that his battles with Phoenix have taught him that trust between attorneys and prosecutors is necessary in order to find the truth. As Maya is reunited with Phoenix, Edgeworth sees Franziska off at the airport.

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.

On New Year's Eve, Phoenix and Maya, along with Gumshoe and the judge, are invited by Avery Richman to ride the maiden voyage of the Silver Star express train.

The details of Richman's original trial state that a secretary-general named Benjamin Cashanova was shot during a year-end ceremony, with Richman found with a pistol in the direction the gunshot came from.

Gumshoe reports about Gale's corpse and the "soul" he saw, which Phoenix reveals was a brief fire that he saw, as the train's cars were actually rearranged just before the takeover.