The story open in London when a young woman named Espella Cantabella is chased by a mysterious force and seeks the aid of Professor Hershel Layton and his apprentice, Luke Triton alongside their friends, Houtarou Oreki, Rima Mashiro and Emmy Altava.
The six are attacked by what appears to be witches; Espella escapes on a cargo freighter while Houtarou, Rima, Emmy, Layton and Luke are seemingly drawn into a medieval town called Labyrinthia via a book called "Historia Labyrinthia" owned by Espella.
Espella is quickly arrested for assault and theft when the freighter docks, following an attack on a freighter staff member.
Phoenix Wright, an American defense attorney from Los Angeles, and his assistant Maya Fey, are in London as part of a legal exchange, and are assigned to Espella's case.
They ultimately deduced that Espella stumbled upon a jewel smuggling operation while on the freighter and was attacked by the supposed victim of the assault. Afterwards, they are supposedly drawn into Labyrinthia through Espella's book as well.
Houtarou, Rima, Emmy, Layton and Luke learned that witches supposedly reside in Labyrinthia, and the town is controlled by the Storyteller, a man who allegedly can turn anything he writes into reality.
The town's Knights of the Inquisition, led by High Inquisitor Darklaw, prosecutes and executes by fire all discovered witches in the Witch's Court.
The Inquisition seeks to locate the Great Witch Bezella, the witches' mythical leader who caused Labyrinthia's devastating Legendary Fire millennia ago. Houtarou, Rima, Emmy, Layton and Luke then discovered Phoenix and Maya, having been brainwashed into thinking they are bakers.
When Espella is accused of witchcraft, she calls on Phoenix to defend her; he successfully disproves the charges, and he and Maya overcome their brainwashing.
As the seven continue to investigate, Layton and Houtarou are attacked by a witch and turned into a gold statue.
Maya is accused of the attack and the murder of alchemist Newton Belduke but Phoenix proved that Belduke committed suicide and Maya did not attacked Layton and Houtarou.
Phoenix also learned that Espella is the Storyteller's daughter as the Belduke's butler is outed as a witch; Espella confessed to being Bezella, so she will not be executed.
Maya rescued Espella, only to be apparently executed in her place while Rima, Emmy, Phoenix, Luke and Espella escaped.
The unharmed Layton, Houtarou and Maya are awaken in a forest outside town, and discovered that a settlement populated by Shades, hooded worshipers of the Great Witch.
The trio then discovered underground ruins where they regroup with Phoenix and his companions.
The seven then discovered the remnants of an ancient civilization that sealed a Bell of Ruin after it caused a disaster.
The discovery caused Espella to suddenly have visions of the Legendary Fire and then declaring herself to be Bezella before fleeing.
When the group returns to town, Bezella appears and seemingly kills the Storyteller with a colossal fire dragon.
Espella is then arrested and charged with the murder, and Darklaw personally prosecutes the case.
Houtarou, Rima, Emmy, Layton and Luke then departed for the Storyteller's Tower to investigate, finding him alive and well at the tower's summit.
Layton then realized that the Storyteller's story is being sabotaged by outside forces.
Meanwhile, Phoenix deduced that Darklaw herself intended to framed Espella when Layton returns and assumes the role of prosecutor, so Darklaw can testify.
Over the course of this final trial, Espella, Darklaw and the Storyteller all take the stand.
The Storyteller's real name is revealed as Arthur Cantabella and he explained that Labyrinthia is an artificial research facility designed to test the human effects of a mind-controlling substance found in the groundwater that causes anyone who drinks it to lose consciousness at the sound of silver being struck, and all of its inhabitants are test subjects who volunteered to have their memories wiped so they could start new lives.
The Legendary Fire occurred when the Bell of Ruin caused the townspeople to simultaneously fall unconscious as a result of these chemicals and the town's fires got out of control.
Believing herself responsible for ringing the bell, Espella became obsessed with the idea that she was possessed by the mythical Bezella, and Cantabella created Labyrinthia's witches and mythology to counteract Espella's condition.
He had the Shades create the illusions of magic and indoctrinate anyone "killed" as a result of witchcraft or the Witch Trials into their number.
Belduke and Darklaw were both in on the project, and Belduke killed himself due to accumulated guilt over the long-term deception.
Darklaw is revealed to be Belduke's daughter and Espella's childhood friend Eve Belduke, who blamed Cantabella for her father's suicide; she lured Layton into Labyrinthia and sabotaged the story to exact revenge on him, and was forced to include Phoenix when he unwittingly got involved.
Phoenix, Houtarou and Layton deduced that she was the one who rang the bell, and repressed the event afterwards.
Eve reconciled with Cantabella and Espella, who finally recovers from her trauma, and Cantabella concluded the Labyrinthia project and lifts the hypnosis.
The townspeople decide to stay in Labyrinthia, and Houtarou, Rima, Emmy, Layton, Luke, Phoenix and Maya all returned to the English mainland.
Afterwards, Phoenix and Maya returned to tackling their usual trials in Los Angeles, while Houtarou, Rima, Emmy, Layton and Luke continued their puzzle-solving adventures in London.
A/N: Inspired from someonestupED, damnlastwords, Jamesdean5842, Hope the Victor and Ace Neptune. All OCs and concepts not created by moi were given permission for me to use by it's respected creators.