This is a list of the mysteries encountered during the investigation.
The Letter from the Future[edit]
"Professor Layton has received a mysterious letter. The sender claims to be Luke from 10 years in the future, but how can this be possible?"
"A grown-up Luke used a time machine to send the letter back to the present, requesting the help of his former teacher, Professor Layton, in rescuing the chaotic future city of London."
The Missing Prime Minister[edit]
"Prime Minister Bill Hawks mysteriously disappeared in the accident at the time machine presentation. What could possibly have happened to him?"
"Prime Minister Bill Hawks, who was unaccounted for after the accident at the time machine presentation, was discovered by Professor Layton in the future London. He was abducted by Dimitri and is now being held prisoner. Will the heroes be able to rescue him?"
Warped London[edit]
"When Professor Layton and Luke emerged from the clock shop, the streets of London suddenly looked quite different. What could have happened?"
"The strange, unfamiliar streets belong to a future London from 10 years after Professor Layton and Luke's time."
"Future London turned out to be a fake city built in an underground cavern beneath the real London. Dimitri led his team of scientists to believe that they were trapped in the future so that they would put every effort into completing a functioning time machine."
Frightened Londoners[edit]
"Many People in this part of London seem to be afraid of Professor Layton. Why would ordinary people who've never met him fear the mild and gentlemanly Layton? It seems to be something to do with his hat..."
"In the future, the city of London is in the thrall of an evil Layton. The sight of the professor, who looks just the same as his future self, is enough to spark fear among the local people."
The Future Luke[edit]
"This young man sent Professor Layton a letter, claiming to be Luke from the future. But how is that even possible?"
"The young man signing himself "Luke Triton" turned out to be an older Luke from 10 years in the future. He wrote to his old trusted teacher to request his aid."
"Future Luke is really a young man named Clive who lost his parents in the time machine accident 10 years ago. He has been planning his revenge on those responsible ever since. He called upon Layton hoping that the professor could save him from his own madness."
Suspicious Individuals[edit]
"A selection of shady characters, all dressed identically in grey, seem to lurk on every street corner in the future London. What are they up to?"
"This shady characters dressed in grey are members of a gang under the control of the future Layton, the boss of the London underworld."
The Evil Layton[edit]
"The future Hershel Layton is a crime lord who terrorises London with his gang of thugs. Known and feared by Londoners as "the devil in the top hat", how could this model gentleman have turned into such a monster?"
"The future Layton turned out to be Dimitri Allen, the famous scientist renowned for his research into time travel. But what was Dimitri's reason for posing as a future Professor Layton?"
Dr. Stahngun[edit]
"Dr. Stahngun is the scientist who unveiled the time machine at the presentation, but no records exist of a scientist with that name. He must be somebody else, using an alias to cover up his true identity. Who is he really?"
"Dr. Stahngun is really Dimitri Allen, one of the scientists involved in the time machine accident 10 years ago."
The Mysterious Woman[edit]
"A woman who looks uncannily like Professor Layton's old sweetheart, Claire, is wandering around town. Who could she be?"
"The enigmatic woman is none other than Claire's younger sister, Celeste. She came to the future London in search of clues as to the circumstances of her sister's death, and is following Professor Layton in the belief that he will uncover the truth."
"Celeste turns out to be Claire herself, sent into the present from the day of her accident 10 years ago. Accepting her fate, she bids farewell to Professor Layton and travels back to her own time, to the day of her tragic accident."
The Men in Lab Coats[edit]
"Men in white laboratory coats seem to be all over this part of town, but the odd thing is that their trouser bottoms and shoes are always soaking wet. What reason could they have for walking around London with wet feet?"
"The white-clad men walking around with wet feet are in fact scientists put to work by Dimitri in his research laboratory. They walk through a partially flooded tunnel under the River Thames to get into town when they want a bit of a break from the labs."