This page or section is in need of more information.
Significant plot details follow.
Raphael (ラルフ, Rarufu) is the main protagonist in Rhythm Thief and the Emperor's Treasure. He is an eighteen year old student in Paris who leads a double life as a infamous thief at night with his faithful dog Fondue. Raphael is nicknamed "Phantom R", stealing valuable artwork only to return it days later. His father disappeared a few years ago. He meets a young girl named Marie after stealing a bracelet bearing the same symbol as a coin his father left him, and finds that her violin has the symbol on it too after helping to defend her from Napoleon's henchmen.
An unknown amount of time before Emperor's Treasure, Raphael's mother died in a car accident. Raphael was very sick as a child. His illnesses forced his father to take up art forgery, painting a copy, then stealing the real work and selling it on the black market, leaving the fake in its place, in order to pay for doctors to look after him. He did eventually get better.
Three years preceeding Emperor's Treasure, Raphael's father left abruptly with no explanation. The only clue to where or why he left was a coin with a strange crest on it. Raphael kept this until he finally found a lead at the Louvre three years later. During this time, Napoleon's casket has been stolen and his father seems to have awaken Napoleon again and serving him.
When Raphael had found Fondue, he was being chased by a cat in an ally. Raphael rescued him, but he didn't like any names he suggested, so Raphael called Fondue "dog" for the time being. The first time Raphael had tried to steal one of his father's fake artworks was unsuccessful. He tried to escape, but there where too many constables in the way. Fondue rescued Raphael in the minigame, Fondue to the Rescue. Afterwards, Raphael decided to keep him and named him Fondue after his love of eating, and after the cheese fondue itself.
Chapter 1: Chance EncounterEdit
Raphael found a new lead that could help him find his father. He enters his apartment and goes into his secret basement. In the basement, Raphael changes into his Phantom R costume and the minigame Showtime is played which starts the game. He then shows Fondue a newspaper article and tells him that this bracelet bears the same mark as the coin his father had left. Back above ground in his room, Phantom R reads the newspaper out loud to Fondue. It says-
"Phantom R: Next Stop, The Louvre!"
"The Paris Constabulary has received a warning from Phantom R that his next target will be the Bracelet of Tiamat. The bracelet, an ancient Babylonian artifact, is part of the Mesopotamia Exhibit on display at the Louvre. Authorities are baffled as to why Phantom R would be after this heretofore unknown treasure. Inspector Vergier of the Paris Constabulary insists it's nothing more than a publicity stunt. He vows to capture Phantom R and put a permanent end to his purloining. Only time will tell if Phantom R is in for the crime of the century or simply in over his head."
Shortly, he and Fondue walks outside of his apartment and comments about the upcoming Fête de Paris. Fondue suddenly runs off and Phantom R finds him next to Madame Paula. When she sees Raphael in costume, she thought that he was getting ready for the Fête de Paris festival. She also mentioned to him that there was another boy living in the apartment, not realizing that Raphael and the boy in front of her are the very same.
Phantom R remembers that he has to go to the Lourve, so he travels North to Musée d'Orsay Station. He runs into a guy named Ghislain, who teaches him about obtaining and using medals at a shop at the Flea Market. At the Flea Market, Phantom R meets Bernard, who wants to complete the legendary Master Instrument. He suggests Phantom R to find a sound if he wants to listen more about it.
After recording the sound of wings from a flapping bat and playing it, Bernard accepts his help and explains that the Master Instrument changes as it hears sounds, which is why he needed someone to collect sounds. Next, Phantom R talks to Auban, who runs Shop Auban. He sells minigames, cutscenes, Phantom Notes, and Sound Disks if you missed any.
Phantom R then heads to Tuileries Garden and finally to the Louvre. He goes to the Main Entry, only to find that Loic, a constable, is guarding the entry. So, Phantom R makes his was to the Denon Wing to sneak inside. After solving a puzzle by tapping on stones in the correct order, a secret passageway opens up and so he enters the museum.
When he enters the museum's first floor, he realizes that Inspector Vergier has installed security cameras. So, Phantom R goes to the security room on the second floor, only to find out that there are more guards too so he avoids them by hiding behind statues in the minigame, Looting the Louvre.
When he finally reaches the security room, Phantom R finds that it is locked with a voice recognition device when Fondue accidentally pressed a button. He finds a sleeping guard and records the sound out him snoring. When playing the recording the machine recognizes the sound to be Joseph's and the doors open. Phantom R then places a dummy clip that is five minutes long to avoid being caught on camera.
Heading downstairs after messing with the camera in the security room, there is a notebook on the floor. It says-
"Press the button and listen well!
Most buttons will have a pair.
You want the one that doesn't."
From this, Phantom R concludes that these were instructions for shutting down the security for something. He then arrives in a room and disarms the security, which was another puzzle, on the Bracelet of Tiamat with help from Joseph's notebook. Finally obtaining the bracelet, Phantom R and Fondue escape the museum at the front
At the front of the Louvre, he is stopped by Inspector Vergier, who wants him to tell everything he knows about an "incident" when he arrests him. Vergier sends the famed Paris Rollerskate Brigade after Phantom R, which leads to the minigame, Le Getaway. Phantom R escapes successfully and finds himself in Place Vendôme. He wonders what "incident" Vergier could be talking about, but he leaves it at that to save the pondering at home.
When making his way home, he has to take a detour since Loic was patrolling Musée d'Orsay Station. When Phantom R passes by Place de la Concorde, a little girl was crying because she lost her balloon. An older girl with blonde hair cheers her up by playing her violin. During the short song she played, Phantom R returns the balloon he retrieved from a tree. Soon after, the constables chased him away quickly and he didn't notice that the mark on the girl's violin was glowing.
Phantom R reaches the Champs-Élysées only to find that another constable was patrolling the place. Eric meets Sarah, a woman who has lost her bulldog. Eric seems scared at the thought of a bulldog, so Phantom R had Fondue to try and bark. It didnt affect Eric at all, so tries to find the bulldog.
Back at Place de la Concorde, a man named Matthias warns that he saw a bulldog on the right of the fountain. When looking at the right side, an older man named Charles explains to him about the Phantom Notes. When they are together, it creates the most wonderful piece of music when played, but no one has ever played it before. Finally, Phantom R finds the bulldog on the left side of the fountain and goes back to play a recording near Eric. Eric becomes frightened and leaves his post.
As Phantom R continues his detour towards home, he goes from FDR Station to FDR Avenue, where a shady guy named Raymond warns that some men in medieval armor are wandering around on the streets. When arriving at Pont Alexandre III, the girl from the park was being chased by someone claiming to be Napoleon and ran towards him for help. The Bracelet of Tiamat starts to glow and realizes that the mark on girl's violin matches the one on the bracelet. Napoleon demands for an object called "the dragon crown."
This leads to the minigame, Battle Diabolique and Phantom R defeats the Chevaliers Diabolique. He then escapes by carrying the girl and traveling across the river by jumping on top of boats.
Chapter 2: On the Trail of the MarkEdit
After crossing the river by jumping on top of boats, Phantom R, Fondue, and the girl land safely on The Seine. The girl thanks Phantom R for saving her. He then introduces himself and Fondue. The girl became surprised for meeting a thief. Phantom R then suggests for her to stay at his place, since he doesn't want her to encounter the knights again. The girl then introduces herself as Marie.
After heading back into his apartment, Phantom R reintroduces himself as Raphael, his regular self. Marie then explains that she doesn't have a family. She was left on a convent's doorstep with her violin by her side. Marie hopes that one day she would become a famous violinist so that her mother would hear her and maybe recognize her.
Raphael then examines her violin since it was resonating with the Bracelet of Tiamat back when they met Napoleon. He finds a hidden switch and the strings began to glow. After solving a puzzle, words appear on the violin-
"The Dragon Crown sleeps at the foot of the Holy Mother, lulled by the princess of the moon."
The two then realize that the words on the violin are connected to Napoleon, since he was saying that Marie had his lost treasure, which was the Dragon Crown. When Raphael inquires about "the princess of the moon," Marie suggests that it could be the title of a song, since the musical score titled "Moon Princess" was also left with her at the convent. The "Holy Mother" part could mean the Notre Dame Cathedral, since the Holy Mother is Our Lady, which translates to "notre dame" in French. He then suggests that they should pay a visit to the cathedral in the morning.
In the morning, Raphael awakes when hearing Marie play her violin. Raphael, Fondue, and Marie head out from the apartment and travel to Rue des Saints-Pères, to Place Henri-Mondor, to Petit Pont, and finally arrive to the Notre Dame Cathedral. Raphael changes into his Phantom R costume and then enters the cathedral.
Inside the cathedral, Phantom R asks Marie to play Moon Princess. After the minigame, Phantom R notices that the stained-glass window is reverberating to the sound of the violin. When solving a puzzle by matching the panes of glass, a hidden compartment opens. Inside, they find the frame of the Dragon Crown.
Napoleon shows up suddenly and tries to take the crown from Phantom R, which leads to the minigame Destroyer Diabolique. Afterwards, the Bracelet of Tiamat starts to glow and the Chevaliers and Napoleon start to float in the air. As Phantom R, Marie, and Fondue escape, they fall to the ground.
After escaping from Napoleon, the trio are back at Petit Pont and Raphael changes into his casual clothes again. He then suggests to take Marie to the convent she lives at, which is called St. Loure. From Petit Pont, the trio travel to the Paris Constabulary, to Rue Livio, to Rue Ramuteau, and finally to Rue des Francs-Bourqeois. A woman named Céline coudn't calm down her baby from crying, not even Marie could calm her down. So, with a recording of a rattle found at Rue des Archives, they manage to calm down her baby and the trio continue to the convent.
When they reach the convent, they meet Jean-François and says that he worried about her. After explaining that Marie was attacked, Jean-François then invites them to come inside, saying that he has good news for her. Inside, Jean-François explains that he found someone who could be Marie's mother. He believes that Marie's mother is Duchess Elisabeth and arranges a meeting with her before the show at the Paris Opéra.
As Raphael leaves the convent, he ponders about the same mark on the bracelet and the one on his coin. He also thinks of why Inspector Vergier keeps on mentioning an incident. Thinking that it's all connected, he realizes that if he looks into this incident, he might find a lead on his father. As a result, he changes into his Phantom R costume again and makes his way to infiltrate the Paris Constabulary in broad daylight.
After hiding behind bushes when playing the minigame Sneaking and Entering, he successfully infiltrates the Constabulary. He then proceeds to find Inspector Vergier's office by relying on Fondue picking up his scent. After entering a hallway, he spots Vergier talking to Loic, a constable, and began to eavesdrop on their conversation. Vergier says that letting Phantom R escape was his fault, and Loic is concerned about him not being able to return home and putting his duty first than his family. Loic also metions that Vergier was working non-stop on this case ever since his wife died. Vergier says that after solving this case, he would have more time with his kid.
After the conversation, Vergier and Loic go their ways which makes a chance for Phantom R to find Vergier's office. Since Vergier's smell spread too much, Phantom R resorted to trying doors. After trying several doors, they finally find Vergier's office. Inside, they find the inspector's office a mess with documents strewn everywhere. Phantom R finds the combination for the safe on his desk, which was 305364.
After solving a puzzle by rhythmically turning the knob of the lock, they find that there were two very thick binders inside. One was a tan binder labeled "R" and the other, a green one, labeled "The Mystère Incident." The first entry was dated 3 years ago-
"I've discovered a link between a string of artwork thefts we thought were unrelated. The link is a mark found on each piece. Why were all the artworks and antiquities which bore this mark stolen? Our investigation so far has turned up nothing. I am grouping these mysterious thefts into one case file: the Mystère Incident."
Phantom R then realizes why Vergier thinks that he is involved with this incident. He also ponders of a name that keeps on popping up in the entries- Graf, but it seems that Inspector Vergier doesn't know who Graf is either.
"Graf is a key player in all of this, as expected. Now there's pressure on our investigation. Graf's doing, perhaps?"
Phantom R then realizes that he doesn't have much time before he is caught, so he reads the last entry before going. The last entry was dated 3 years ago and the location is Les Invalides. The item stolen was Napoleon's casket. Phantom R then remembers that the guy who attacked Marie called himself Napoleon. Now that he had read about the incident, he then made his way to escape from the Constabulary.
Phantom R exits at the Constabulary Back Door and soon encounters a football being kicked at him. A guy introducing himself as Charlie appears from behind a tree and states that intruding the Constabulary is prohibited. Charlie then gives Phantom R two options: to come quietly or to recieve a penalty kick to the head. Phantom R chooses neither, so Charlie challenges him to a football match, which leads to the minigame Charlie Takes the Field. Phantom R beats Charlie and so he and Fondue escape.
Chapter 3: The Darkness of Les InvalidesEdit
Phantom R and Fondue are still at the Constabulary Back Door. Since the last case of the Mystère Incident was at Les Invalides, Phantom R deduces that there might be some clues there relating to the case so he might find his dad. So, he makes his way to Les Invalides.
As Phantom R travels to Rue de Conti, he meets a reporter named Colette from the Eiffel Bugle, wanting an "opinion from the street" ahout Phantom R. He manages to escape her questioning and she doesn't realize that she had just tried to interview the infamous thief himself.
When Phantom R finally reaches Les Invalides, he goes inside and Fondue catches the Chevaliers' scent from underneath the casket. When examining the casket, Phantom R finds a trick lock and disarms it. After disarming the lock, Phantom R discovers an underground passage. He and Fondue then venture underneath the hidden passageway.
The passageway was so long and going through required tricky footing, which leads to the minigame Onward Through the Dark. After playing the minigame, Phantom R finds himself in the catacombs underneath Paris. The torches were lit, and he soon hides and eavesdrops because two knights of the Chevaliers Diabolique were passing by. They discuss that Graf was coming to their hideout and need to get ready for his arrival. After the Chevaliers pass by, Phantom R continues down the passageway.
Soon, Phantom R comes to Napoleon's room and hides to hear what Napoleon was saying. Napoleon is sitting in his chair and there is someone standing behind him, but it was too dark to see. Napoleon was discussing the plan with the shadow behind him that the Dragon Crown needed to be complete with the Queen's Pendant and the Cross of the Sun King. Phantom R recognizes the shadow's voice. He jumps from his hiding place and shouts, "Father!" He realizes that his father was working for Napoleon for the 3 years when he was missing. Napoleon grows angry at him for not giving him the Dragon Crown, which leads to the minigame Napoleon's Hideout. Phantom R successfully beats the Chevaliers Diabolique yet again and runs outside of Les Invalides.
By now, it was night time and he was so shocked to find out that his father was working with evil people. Since his dad was working with Napoleon, Phantom R though that getting the treasure first would track his father down. Since the Dragon Crown wouldn't be complete without the Queen's Pendant and the Cross of the Sun King, Phantom R decides to go after the pendant first. Since he needs info about the pendant, an antiquarian would help. It just so happens that he read an article about an antiquarian at the Sorbonne, so he travels there.
When Phantom R arrives at the Sorbonne, he tries to find the antiquarian. He asks a student named Rosalie, who points to the sleeping middle-aged man who just happens to be her professor. Alàn, the sleeping professor, didn't wake up when being called. So, Phantom R played the recording of the sound of a rooster found at The Market to make him think that its morning. Alàn wakes up and when he was just about to give advice, he remembers that he needed to go somewhere. Alàn then recommended for Phantom R to go to the Paris Archives and look in the book titled Traditions and Treasures of the Royal Family.
When he arrives at the Paris Archives, the librarian named Vanessa informs him that Traditions and Treasures of the Royal Family is in the special collection, which only members of the Société Académique can go in. Since Phantom R isn't a member, he records the ringing of a phone to distract the librarian so he could go into the the room where the special collection is kept.
When Phantom R tries the door to where the special collection is kept, it was locked by a mechanism. After solving the puzzle, Phantom R enters the room and finds the book on a shelf relying on Fondue to sniff out the professor's scent. After finding the book, Phantom R finds out that the Queen's Pendant was owned by Marie Antoinette and the diamond in the center is called the Queen's Tear. He also finds out that the current owner is Duchess Elisabeth. Since Elisabeth is Marie's mother, it could explain why Napoleon attacked her. Phantom R then heads back to his apartment to think.
Back at his apartment, Phantom R ponders about the Queen's Pendant, Duchess Elisabeth, and when Marie was attacked. It can't be a coincidence that they are all related! Since Duchess Elisabeth currently has the pendant, he has to get the pendent first before Napoleon. Phantom R then says that he will give the Inspector a heads up on intruding the Opéra. So, he decides to head to the Opéra tomorrow.
Chapter 4: The Paris OpéraEdit
Raphael wakes up in the morning and wonders if the Duchess and Marie really mother and daughter and the connection between the Queen's Pendant and Napoleon. He also hopes that his heads up to Vergier would help avoid the worse. He then goes out with Fondue and travels to the Opéra.
Inside the Opéra, a man named Julian checks the ticket of a woman named Lorraine. Raphael then realizes that you can't get in unless you have a ticket. So, he goes outside to find a place still selling tickets.
Outside a man named Cyril is talking to himself about keeping his tickets safe in his attaché case, and that with a combination like 614253, no one will be able to get it open. Raphael then asks him if there is any place still selling tickets for the Paris Opéra. Cyril then says that he has some tickets in his case, which Raphael questions where he got them from. Cyril really wants Raphael to buy one, but he doen't want to do anything illegal. So, he rejected him for not buying one.
Since Raphael felt sorry for him, he went and got a recording of a police car siren to scare him away.After scaring Cyril, he left behind his attaché case. When disarming the lock on the case, Raphael was able to get the tickets. So, he goes back to the Opéra.
Inside, Julian checks his ticket. Raphael was then allowed inside the Opéra as he planned. As he was walking through, he sees Jean-François talking to Inspector Vergier about the notice he had sent earlier. According to what Vergier said, Phantom R has warned him that he will come and take the Queen's Pendant worn by Duchess Elisabeth. When Jean-François questions about who Phantom R is, Vergier explains that he is a thief that steals artwork and returns them the next day without a scratch. Jean-François doesn't seem to care at all about him and only cares that the Duchess is safe.
After eavesdropping the conversation, Raphael then wonders if Marie has met her mother yet, so he goes and searches for Marie. He goes to the seating area and sees that Vergier and Loic are yet again engaged in conversation. Loic reports that there are no suspicious people seen so far. Vergier says that Charlie should just leave Phantom R to the police.Thinking back, Raphael recalls that a boy named Charlie approached him, which explains why he was hanging around there now that Raphael knows that he is Verigier's son.
After Vergier and Loic leave, Raphael notices that he dropped something. When he picks the item up, it appears to be a Vergier family photo with Vergier, a woman that appears to be Charlie's mother, and Charlie as a baby. Thinking that it will be useful, he holds onto the photo.
Then, Raphael sees Marie, the Duchess, and Jean-François. Elisabth looks at Marie for a brief moment before climbing up the stairs and says that Jean-François was wasting her time for saying that Marie was her daughter. In the middle of Elisabeth's ascent, Marie suddenly starts to play "Moon Princess" on her violin. After finishing the song, Elisabeth pauses for a moment before saying to Alfred, her butler, that they were leaving. After Elisabeth rejected Marie, she ran down the steps crying.
Afterwards, Jean-François asks why Elisabeth had rejected her even though he did so much research to find Marie's mother. Elisabeth warns Jean-François to not blow it and then goes with Alfred to her seats to see the opéra.
Raphael then works with Fondue to find out where Elisabeth will sit during the opéra. He then runs into Clément during his search, saying that only VIPs are allowed past him. Raphael then deduces that Elisabeth most likely is a VIP, so he creates a plan to become an employee to slip into the place. He overhears Andre, who was talking to himself that they were short handed on waiters and making him very busy. Raphael realizes that this is his chance, so he goes to Clément to take his test to qualify as a waiter.
When he finds Clément, he seems to forget something and needed to hear a "binging" sound to remember. When talking to Andre, he says that Clément usually forgets things and advises that Raphael should get Clément to listen to a bell. At the entrance, there is a doorbell on a desk, and Raphael records the bell. When he plays the sound of the doorbell near Clément, he remembers that he forgot to pay his staff on payday. Raphael is then able to take his test.
After passing the minigame, Hurry Up and Wait, Clément orders Raphael to bring drinks to the VIPs. Raphael then whispers his plan to Fondue, and they split up. He continues to head towards the VIP salon and Andre congratulates him. He warns Raphael not to mess up as he enters the salon.
When Raphael delivers the drinks to Elisabeth, Alfred starts to question him, since he knew everyone in the staff. When he just came to a conclusion that the new waiter is Phantom R, Loic downstairs suddenly shouts that a wild dog has appeared. It is then shown that Fondue is biting the constables' butts in the minigame, Phantom Fondue. During the confusion, Raphael changes from his waiter uniform to his Phantom R costume.
When he goes to Elisabeth, he is blocked by Alfred. Elisabeth makes a bet that if he beats Alfred, he could get the pendant. Phantom R then defeats him in Throwdown with Alfred and gets the pendant. Elisabeth then says "Since ancient times, that bracelet has been worn by the one chosen to do Tiamat's will here on Earth." She also shares a family saying to Phantom R:
"Beneath the sun and moon, Amaryllis leads those who sing in the rain."
When Phantom R was about to question if she really wasn't Marie's mom, he gets interrupted by Inspector Vergier. He runs away for the time being and tries to look for an escape route. Since a constable is blocking the front entrance, he then thinks escaping through the roof would be good. When he goes to where the seats are, Eric is guarding the place and sounds scared after hearing the rumors of ghosts in the Opéra.
After recording the sound of a ghost and playing it near him, Eric flees, so Phantom R can escape easily. He then climbs his way to the roof after playing the minigame, Phantom from the Opera. When he reaches the roof, he is interrupted from looking at the view of the city when Charlie comes flying down on a hang glider. Charlie then challenges him to another soccer match, which leads to the minigame, Rematch with Charlie.
During the match, Charlie loses his footing and is now hanging over the side of the building, holding on to his life. He claims that he would rather die than be saved by Phantom R. When Charlie was about to fall to his death, Phantom R grabs his hand and pulls him back on the roof. He then makes his exit by jumping off the roof and disappearing from Charie's sight.
Chapter 5: In Search of MarieEdit
Phantom R is on the ground in front of the Opéra after defeating Charlie again. Worrying about Marie, he changes back to his regular clothes and tries to find her. So, he starts asking around to see if people have seen a girl with a violin.
Starting at Rue Danielle Casanova, Raphael talks to Benoit who tells him the girl ran to Place Vendôme. He meets Cedric, who is chubby and eating macaroons. He recalls that she was wearing a vanilla-white cardigan and was heading for Tuileries Garden and he nearly dropped his sweets when she ran past. Next, Raphael speaks with Maxim, who sells balloons. He tells him that the blond girl was running towards Musée d'Orsay Station while crying. Then, he talks with Grace, who tells him she ran towards the apartments.
When Raphael reaches the front of his apartment, he runs into Madame Paula, who commented that she looked very sad when she looked at his apartment when she ran past. She tells him that the girl ran towards Rue des Saints-Pères. From that, Raphael thinks that Marie ran back to the convent. When he speaks to Jean-François, they both agree to split up and search for her.
As Raphael continues his search for Marie, he runs into Marie's best friend at the convent on Rue Ramuteau.
His clues lead him to Montmartre. Fondue runs up to Marie wearing Phantom R's hat. Phantom R takes the hat off of Fondue. He then tells her "If you do it right, you get the angels. You're an angel, so maybe they'll come." Thus begins a rhythm game similar to the first. Afterwards, Phantom R and Marie go back to his apartment. He shows her the secret cellar holding all the forgery art his father made. Then there is a flash back to fifteen-year-old Raphael, running after his father in the snow. His father gets into a car and drives away. Raphael noticed a coin on the ground and saw the mark on it. He then decided to fix all his father's doings and return the real works of art not yet sold. After the flash back, Raphael takes Marie back to the convent, where Marie then asks if she can go with Raphael and Fondue. Although he refuses at first Raphael lets Marie join him and Fondue.
Chapter 6: Intrigue in the ShadowsEdit
Marie and Raphael arrive in the Palace of Versailles. When they arrive they notice that a lot of people are dressed very nicely and that there's a party in the palace so they plan on going in and finding what they are looking for. However they then realize that you need to have an invitation to get in, in the end they get a ticket by doing this: Raphael starts talking to a man named Charles and he notices that Marie has a violin so he asks her to join the orchestra that is playing at the party and he also let's Marie bring Raphael to. When they enter the palace Raphael and Fondue start searching the palace. However much to Raphael's shock he sees his father, Issac so he and Fondue start following Issac. But sadly they lose sight of him so they give up on their chase and they head into the ballroom to look for Marie, Marie then appears in a dress. Raphael blushes at the sight of her and then asks her to dance with him (hinting that he may have romantic feelings for Marie), which she says yes to. After they share their romantic slow dance they go out into the garden, they notice that there are golden frogs on the fountain and both Marie and Raphael remember an old nursery rhyme so they play it, then suddenly the cross of the sun king appears. However Napoleon arrives to take the cross but Raphael fends him of while Marie leaves to get help, while Marie goes to get help she runs into someone but he turns out to be one of Napoleons goons. Napoleon and his goons then take Marie away telling Raphael that "You have until tomorrow at noon to give me the cross and you will get the girl back."
Chapter 7: Saving MarieEdit
With Napoleon holding Marie hostage, Raphael has no choice but to finish the Dragon Crown in order to save Marie. But Raphael really needs the cross and Marie so he sets out to find Charlie. However when Raphael finds Charlie he is shocked to find out that he is actually a girl named Charlotte. Charlotte refuses to help Phantom R as she sees him as an enemy, but Raphael manages to persuade her into helping him. When Raphael reaches the top of the Eiffel Tower he meets Napoleon and gives him the cross. However Charlie stops him right in the nick of time, as Raphael rescues Marie they are both stunned to see Marie's guardian, Jean-François. He then does the most surprising thing - he shoots Raphael. He then takes the Dragon Crown from the wounded boy and just as he is about to kill him Charlie stops him and flies Phantom R to safety.
Chapter 8: Marie's SecretEdit
Charlie tries to wake up a nearly dead Phantom R when he wakes up he decides to go and look for Duchess Elizabeth so he can ask her a few questions. However he fails to get into her home because he needs an appointment, but he manages to trick a hungry servant and he gets in a back entrance. When he gets in the house he looks for some clues from Marie and Elisabeth's past. He realizes that they really are mother and daughter, when he arrives downstairs he sees that Alistar has been beaten up by Napoleons Chevaliers Diabolique and they took Elisabeth! Meanwhile inspector Vergier fends off the Chevaliers Diabolique. And Elizabeth and Marie meet again Napoleon tells Marie to play her violin or Elisabeth will die so Marie does this, which much to everyone's shock the earth shakes and the Hanging Gardens suddenly comes out of the ground.
Chapter 9: Weapon in the CloudsEdit
After the Hanging Gardens rise from the ground Raphael climbs up it and gives chase to Napoleon. When he reaches Napoleon he attempts to shoot Raphael but instead he turns his gun to Marie, when he pulls the trigger Elisabeth steps in shielding Marie. With Elisabeth in a now near-death situation she confesses that she is Marie's mother and she presumably "dies", Marie weeps over her mum saying "Mother, no! Please don't leave me again, oh mama, Mama!" Napoleon then leaves with Jean-François and Raphael gives chase leaving Marie with Fondue and Vergier. When Raphael enters a volcanic part of the castle Jean-François reveals that Raphael's father Issac has been working for them. Raphael and Jean-François then battle each other, after this Raphael finds Napoleon and they face off in the last battle. When Raphael beats Napoleon he reveals his real name Leonard Bonar. Leo then falls to his death and Raphael tries to stop the place from exploding. Marie comes and encourages Raphael with a song, Raphael then barely saves the day and they escape. At the end of the chapter Raphael, Marie and Fondue are seen watching some fireworks go off and Raphael holds Marie's hand and says "It's all over Marie there is no one in this world that can do anything to hurt you."
Chapter 10: Parting WaysEdit
In this final chapter after Raphael saves Paris from "Napoleon" and Jean-François, Raphael goes to talk to the Duchess Elisabeth. Elisabeth tells Raphael that she and Raphael's father, Issac were good friends but she doesn't know were he is, Elisabeth also thanks Raphael for saving Marie, who then comes in and thanks Raphael, she then begins to cry because they are parting ways. Raphael holds Marie's hand and he says "It wasn't me that changed your fate it was you." As Marie begins to wipe her tears away, Raphael then takes her outside saying "It's time for the last dance and I want to dance with you, then it's au revoir." And so they dance together, they say their goodbyes and Raphael leaves. In the last few minutes Marie sates that she will never forget Raphael, also Raphael's father, Issac, is seen talking to the real Napoleon stating that the real fight is just beginning and for Raphael to be ready for it. At the end of the chapter Marie is seen performing with her violin on a stage as Raphael and Fondue watch from the background, and Raphael states that he can't wait to see her perform in all of her concerts. But Inspctor Vergier and Charlotte (Charlie) see him and they chase him. The final scene shows Marie (who noticed Raphael) smiling and Raphael and Fondue being chased by Vergier and Charlie.
Raphael: My father taught me a lot, like never take stuff that doesn't belong to you. And before you ask, no this art doesn't belong to me. It's a long story.
Raphael: If you do it right, you'll get the angels!
Raphael: You're an angel, so maybe they'll come!
Phantom R: Do you know where I can find Inspector Vergier?
Constable Eric: Inspector Vergier? I am very sorry, but, uh, I'm afraid I can't divulge that information.
Phantom R: I'm an honest, taxpaying Parisian. Don't I have a right to know?
(Paris Constabulary, Chapter 7)
Phantom R: Too close! (when he gets rank D at the end of a minigame)
- Raphael got his unique sense of rhythm from his mother, as she was a ballet dancer. When Raphael was young, she died in a car accident.
- There are two similarities to other characters.