A second season adapts the 3rd game in franchise, Trials and Tribulations, as well as "Lost Turnabout", the only case from the second game that was not adapted in the first season.
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.
When the Kurain Village's sacred urn is stolen from an exhibit at the Lordly Tailor by the mysterious thief Mask DeMasque, Phoenix, Maya, and Pearl investigate the scene and meet self-proclaimed ace detective Luke Atmey.
As Phoenix struggles to make a case that Ron wasn't the one who stole the urn, Maya brings in Larry, who was working as a security guard for the exhibition.
After Phoenix and Maya notice that her urn has been covered in splotches and returned to its original shape, Adrian reveals she accidentally broke and tried to cover it up by moving a statue, which was in different position to when Phoenix first found it.
Resuming their investigation at Trés Bien, Phoenix and Maya learn that Armstrong owes money to a loan shark. After getting more details from Kido, Phoenix and Maya visit the office of the loan shark in question and the one who impersonated Phoenix, Furio Tigre.
Following a hole-filled testimony by Armstrong, Phoenix suspects that the murder Kido witnessed was actually a reenactment which took place after the actual murder.
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.
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.
After accidentally breaking a precious seashell that she received from Maya, Pearl asks Phoenix to help her search for an identical looking shell without Maya knowing.
One year prior to her first meeting with Phoenix, Mia takes on her first client; a death row convict named Terry Fawles who is accused of murdering policewoman Valerie Hawthorne, with the assistance of her senior, Diego Armando.
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.
While investigating the shrine, Edgeworth listens to Bikini's account of Elise's murder, learning that Pearl has gone missing, before meeting up with Larry, who appears to be hiding something he saw on the night.
During his testimony, Larry presents a sketch he drew of what he saw on the night of the murder, allegedly depicting Iris flying over the flaming bridge.
While Iris is brought in to work on the trick lock, Phoenix finds a charred letter instructing someone to channel someone, along with a talisman Elise was carrying.
As court resumes with Phoenix once again against Godot, Iris suddenly claims that she helped cover up Elise's murder after she was allegedly killed by Maya in self-defense. However, her testimony proves false with the reveal of real murder weapon and Elise's identity as Misty.
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.
