The prologue starts with a young Victor Frankenstein witnessing a public demonstration of his father's research to bring the dead back to life. Unknown to them, the experiment has been tampered with, leading to a massive failure and the downfall of the Frankenstein family. Victor then swore to finish his father's research and obtain the recognition they deserve.
The story proper starts with chief police detective Eva Schmitz encountering multiple mysterious cases, which seem to be connected to the mysterious organization Aegyptus. In addition, Elizabeth Lavenza, the daughter of the victims of one of the cases, seem to be wandering around with an agenda of her own.
Frankenstein provides examples of:
- Action Girl: Elizabeth is a skilled fencer. In one scene, using her wits and fencing skills she manages to save Stoneboy from a gang of pirates by herself.
- Adaptation Inspiration: A scientist named Victor Frankenstein created an artificial humanoid monster. That's about the only thing this story has in common with the original novel. Oh, and some characters have the same names as characters in the novel.
- Back from the Dead: The executed Huxley came back as a humanoid monster with no memory.
- Big Bad: Samuel, the leader of Aegyptus. He killed the Lavenza couple and framed Huxley for it, thus starting the conflict of the story.
- Decoy Protagonist: The first two chapters follow Schmitz as she encounters various cases. But afterwards you play as different characters, with Schmitz only occasionally being the center character of the scene. Then she dies at the end of chapter 5, disappearing from the story afterwards. The real protagonists of the story are Elizabeth and Huxley.
- Defector from Decadence: Samuel, the leader of Aegyptus, employed Victor Frankenstein to create a new body for him to live forever in. Victor didn't want to follow the order, so he used the body to revive Huxley instead in hope he can stop Samuel's plans. Turns out the part about Victor is a lie, as Samuel and Victor are the same person all along.
- Immortality Seeker: Samuel wants to transfer his mind from his aging body into a new, stronger body so that he can live forever.
- Memory Gambit: Victor transferred his brain from his aging body to the Creature's body, knowing he would lose his memories. He left hints to lead the Creature to Babel together with Elizabeth, recovering his memory, and live for eternity. This bites him back in the ass when the "Huxley" identity doesn't disappear even when Victor's memories come back, causing the Creature to have two personalities.
- Once More, with Clarity!: In general, the early chapters introduce the mysteries by having Schmitz investigate cases and other characters. Later chapters show the same events but from the other characters' perspectives, clarifying what they really are doing.
- In chapter 1, Schmitz encounters a case where someone has broken through a morgue. In chapter 3, you play as the revived Huxley breaking through the morgue. The same thing happens with the Neumann office case.
- One scene has Schmitz tails Elizabeth as she goes around wandering the city for some reason. Later you play as Elizabeth wandering around the city, as she's looking for clues to Henry's whereabouts.
- Small Role, Big Impact: Schneider only appeared in one scene in the prologue. Yet, him tampering with Alphonse Frankenstein's experiment is basically what throws the entire plot into motion.
- Super Strength: Huxley's revived body is huge and very powerful. He killed an unfortunate hunter in just one punch.
- Star-Crossed Lovers: Elizabeth is a wealthy noble lady, Huxley is a poor painter. Her parents don't approve of their relationship, which allegedly causes Huxley to murder them.
- Together in Death: The very last scene of the game, after the credits roll, is Victor reuniting with his family in the afterlife.
- Tomato in the Mirror: The Creature you've been following isn't Huxley at all, but an amnesiac Victor who transferred his brain into the monster's body.