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?!

A shocking murder leaves Mayoi (Maya), little sister of Chihiro (Mia), in a situation Naruhodo (Phoenix) cannot ignore.

The trial for the chief's murder begins. Will Naruhodo (Phoenix) be able to get Mayoi (Maya) out of this?

The case reaches its climax, as Naruhodo (Phoenix) and Konaka (White) look to get each other convicted.

Popular television hero Steel Samurai is arrested for murder, and it's down to Naruhodo (Phoenix) and Mayoi (Maya) to defend him.

The investigation on the Steel Samurai case turns to a new direction, as the security lady's information gives our attorneys a valuable lead.

Will the true culprit of the Steel Samurai case be caught? And why did they do it?

The body of a man shot dead is found in Gourd Lake, and the suspect is none other than...

The trial begins, and the god of prosecutors immediately shows off his immense prowess.

Things are looking desperate, as a guilty verdict looms on the horizon. Will the secret behind this case be revealed?

Will the defense be able to prove the guilt of the real culprit? And how will they do it?

Turnabout Goodbyes reaches to its shocking conclusion!

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

A while after the last case, a new client arrives with the request to attend a channeling ritual.

Gumshoe gives his testimony, explaining that Grey was first stabbed before being shot by his own pistol. He presents Maya's ceremonial robes, which are covered in blood and have a hole in the sleeve. While Franziska claims that bullet hole is irrelevant, Phoenix notices the hole is missing a gunpowder burn that would appear if it was shot at close range. Lotta is then brought to the stand, presenting the photo she had taken of "Maya" when entering the crime scene. Phoenix notices that the person in the photo is missing the head ornament Maya was wearing, believing that another person was impersonating Maya. As Phoenix struggles to prove how this additional person entered the locked room, Pearl manages to channel Mia, who reminds Phoenix of the room key Pearl gave him, which proves the possibility of another person.

While returning to Kurain, Pearl explains to Phoenix how, when the murder took place, she was in an outdoor walkway trying to repair a sacred urn that she had accidentally broken. After speaking with Morgan, who explains how Maya was supposed to be next in line to inherit the channeling school following Misty's disappearance, Phoenix finds a piece of Maya's outfit in the incinerator where Pearl found the key. Coming across Lotta again, Phoenix finds a clothes basket with a hole in it, while Lotta gives him information on Ini, revealing she was in the same car accident as Mimi and had to undergo reconstruction surgery. As Phoenix questions Ini about the incident, Morgan goes with the police to join the investigation. On the second day of the trial, Phoenix asks Pearl to channel Mia again so that she doesn't hear what happens during the trial. The trial begins with Morgan testifying against Maya, claiming she fled from the channeling room after committing the murder, before Ini is brought to the stand.

Ini claims that Maya, possessed by Mimi, came to see her in the side room following the murder. However, Phoenix finds this claim to be false, as she would have encountered Pearl trying to fix the urn in the walkway. Putting together the evidence, Phoenix deduces that Ini was hiding in the clothes basket in the channeling chamber, where she knocked out Maya and stabbed Grey, who used the last of his strength to try and shoot her. He further deduces that Morgan was her accomplice, helping her to frame Maya and dispose of evidence. Tasked with finding a motive for committing such a complicated murder, Phoenix questions Ini about the car accident, deducing from her statement that she is actually Mimi, who had been reconstructed with Ini's face following the accident that took the real Ini's life. Mimi reveals that she had hoped to escape her history of medical negligence following the accident, but when Grey's decision to hold a channeling ritual threatened to expose her, Morgan came up with the murder plan in order to frame Maya and have Pearl become the head of the Kurain school. Following the trial, as Morgan is arrested and the channeling school is temporarily closed, Pearl encourages Maya to return to Phoenix's side.

Phoenix and Maya go to see the Berry Big Circus show headlined by magician Max Galactica. The next day, they discover that Max has been accused of murdering the circus' ringmaster, Russell Berry, though Max states he is innocent, as he was discussing his salary with him. After meeting Berry's daughter, Regina, Phoenix and Maya hear about the crime from Gumshoe, who claims that Max's ability to fly places him as the prime suspect as only the victim's footprints were found. Finding that most of the staff seem to also suspect Max because of his cocky attitude, they hear from Moe the Clown that Max allegedly hit Ben the ventriloquist with a bottle the other day. While looking through Berry's office, they find the contract that Max had mentioned to be dated a week prior to the meeting. Phoenix threatens to drop Max's defense, prompting Max to confess his strained relationship with the other performers, convincing Phoenix to change his mind. Phoenix ends up chasing a monkey to one of the performer's rooms, where they find a bust of Max and a diamond ring, which allegedly belongs to Ben's puppet, Trilo. Speaking through Trilo, Ben claims that he saw Max heading to the crime scene on the night of the murder, but Phoenix points out that he would've had to see the ringmaster too. Trilo rebukes Phoenix, saying he wasn't the only witness to the incident.

As the trial begins, Gumshoe explains the strange circumstances of the case before Moe is brought to the stand as a witness, claiming that he saw Max flying off outside his window moments after Berry's murder. After the trial is postponed so that the prosecution can investigate how the murder occurred, Max reveals that he lent Berry his costume on the night of the murder. Revisiting the room they came across the previous day, Phoenix and Maya meet Ken "Acro" Dingling, an acrobat who lost the use of his legs six months ago, but he is dragged away by Franziska, who reveals she wants revenge against Phoenix for defeating Edgeworth. After hearing from Moe that Berry was angry about something on the morning of the murder, Phoenix checks his office and finds a threatening letter pertaining to an incident six months ago, calling Berry to the place where he was murdered. Asked about the incident, Moe explains how Acro's brother, Bat, was put into a coma by Regina's pet lion, Leon, who was then shot by Berry. Regina then reveals that she found the note while returning from Acro's room, leading Phoenix to suspect the note may be from Acro. As the trial resumes, Phoenix accuses Acro of being the one who plotted Berry's murder.

Phoenix deduces the mystery behind the crime scene, explaining that a bust of Max was dropped on Berry's head when he attempted to open a heavy box. When the bust was pulled back up, it latched onto Max's costume, leading Moe to mistake it for Max himself. Believing Acro, who lives directly above the scene, is the only one who could have committed the crime, Phoenix brings out the threatening note, explaining how it relates to the incident six months ago. He reveals that the reason Bat was attacked was because the scarf Regina gave him was covered in pepper, which caused Leon to sneeze and bite down on him, meaning that Acro's intended target was Regina. As the decisive evidence, the bust, appears to be nowhere to be found, Phoenix deduces that Acro has been hiding it inside his wheelchair, leading Acro to admit his guilt. Afterwards, as Moe takes over as the Big Berry Circus' ringmaster, Gumshoe gets in contact with Edgeworth.

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.