Day 1 - Trial
Athena Cykes is standing in the defendant lobby, anxiously waiting for the trial of her close friend Juniper Woods to begin. Juniper is accused of blowing up a bomb in Courtroom No. 4 of the District Court. In stumbles Apollo Justice, very badly injured as a result of the bombing and on the brink of collapse, desperate to lead the defense and find Juniper Not Guilty. However, Athena convinces him that he's too injured to take the case and instead she offers to go in by herself as her first solo trial.
As the trial begins, Athena finds herself facing off against the "Rookie Humiliator", Gaspen Payne. Payne is a snide and arrogant man who quickly pushes Athena's buttons. The prosecutor lays out the state's case: Juniper Woods is accused of detonating a bomb concealed inside a stuffed animal and resulting in the death of a detective who was helping evacuate the courtroom, Candice Arme. Athena stands ready to begin her counter the arguments but finds herself paralyzed with fear with flashes of a trial from her childhood rushing back to haunt her. The case almost seems lost until the courtroom doors burst open and the legendary turnabout attorney Phoenix Wright enters the courtroom. He informs Athena that Apollo called him down and he takes over the case, pointing out critical points that the prosecution did not address and must be further examined before a verdict can be handed down.
The first witness called to the stand is Ted Tonate, a member of the bomb squad for the police. He claims that he saw the bomb activate, so he was able to warn everyone else in Courtroom No. 4. Phoenix points out the bomb was in a stuffed animal, so Ted shouldn't be able to tell. Tonate corrects himself by saying that he heard the bomb activate.
Juniper is then called to the stand, but she has trouble trying to testify about the events surrounding the bombing due to her fear. Using the Mood Matrix, Athena is able to display Juniper's actual emotions, giving Phoenix a way to jog Juniper's memories. Juniper first remembers how Apollo saved her during the explosion, then recalls that she lost her Bum Rap Rhiny doll during the evacuation. With this new information, Phoenix points out that the evidence pointing to Juniper, a vinyl tail with Juniper's fingerprints, could actually belongs to her Rhiny doll and not the Phony Phanty doll that contained the bomb.
Court is adjourned for the day. Phoenix and co head for the ruins of Courtroom No. 4, where Apollo is searching for evidence. However, to their horror, they only find the attorney in red unconscious on the damaged floor.
Day 2 - Trial
Juniper's trial resumes with both Phoenix and Athena both despondent over Apollo's assault. Payne then surprises everyone by claiming that it was Juniper who attacked Apollo in order to cover up her role in the bombing. As proof, he shows a picture of bloody writing that was found next to Apollo, and it says "WOODS". Payne says Apollo had written the name of the person who attacked him.
Juniper is called to testify about what she and Apollo did yesterday in Courtroom No. 4. Juniper states that before she called to testify, she and Apollo were there to search for her Bum Rap Rhiny doll, and Apollo first checked the area around the witness stand. Phoenix points out that there's a large piece of debris in front of the witness stand, so Apollo couldn't have searched there. Another photo is presented into evidence that shows the "debris" is really the bomb transport case that was used in the trial that got interrupted by the bombing. Juniper recalls that she actually saw the case to the right of it's current position, which would place it on top of the bloody writing Apollo supposedly wrote.
Phoenix declares that it meant Apollo didn't write anything in blood, as the case would be in the way. It was only moved after Apollo was knocked out, as indicated by the tire tracks on his bandages. But it couldn't be written by the culprit, as Apollo didn't bleed enough to have enough "ink", as it were. Phoenix suggests that it could actually be Candice Arme, the bombing victim, who wrote the message, and that she actually wrote "L10015", aka Ted Tonate's ID number. Phoenix claims that Candice was trying to point to Tonate as the real criminal and Tonate, being the first person to discover her body, had the opportunity to cover up the message with the bomb transport case and later alter the message to read "WOODS" when Apollo was searching the courtroom.
Ted Tonate is called back onto the stand, while a DNA test on the bloody writing is performed. Tonate claims that he found Arme's body near the entrance by some pointy rubble, but Phoenix notes that the autopsy report says something flat struck Candice's head. The DNA report then comes in, confirming that Arme wrote the message. Tonate is forced to admit that he saw "L10015R" written in blood, and states that Arme was mistaken about him being the bomber. Phoenix jumps on the fact that Tonate saw his full ID number, since this means it had to be written before the explosion, as there was only partial traces of an "R" due to the floor being broken in that location.
Phoenix declares that Candice Arme actually died before the bombing, and states that Tonate bludgeoned her with the bomb itself, since it had a cube-like shape with flat surfaces. Tonate points out that the bomb blew up, meaning Phoenix can't prove it. Phoenix realizes that Tonate had to hide Candice's body before the trial began, and accuses Ted of hiding the dead detective in the bomb transport case. Cornered, Ted threatens to blow everyone up if he isn't allowed to leave in peace, claiming the "training bomb" he was holds is actually the bomb from the other trial, and the bomb that blew up the courtroom was something he built. This scares Payne and the spectators into fleeing. However, Phoenix calls his bluff, pointing out the real bomb had a cracked display as a result of it being used to kill Arme. For the coup de grace, Phoenix opens the bomb transport case to reveal blood stains.
After breaking down, Ted Tonate finally confesses, saying that Arme caught him trying the steal the bomb for himself.
The trial is finally over, with Juniper declared not guilty. But there is still one mystery left unsolved. What happened to the remote switch used to trigger the bomb?
Behind the Turnabout