On a stormy night, Percy Bysshe Shelley and Lord Byron praise Mary Shelley for her story of Frankenstein and his Monster. She reminds them that her intention for writing the novel was to impart a moral lesson, the consequences of a mortal man who tries to play God. Mary says she has more of the story to tell. The scene shifts to the end of the 1931 Frankenstein, in 1899.

Villagers gathered around the burning windmill cheer the apparent death of the Monster. Hans, the father of the girl the creature drowned in the previous film, wants to see the Monster's bones. He falls into a flooded pit underneath the mill, where the Monster—having survived the fire—strangles him. Hauling himself from the pit, the Monster casts Hans' wife to her death. He next encounters Minnie, who flees in terror.

The body of Henry Frankenstein, who is thought to have died at the windmill, is returned to his fiancée Elizabeth at his ancestral castle home. 

Henry visits the lab of his former mentor Doctor Septimus Pretorius, where Pretorius shows Henry several homunculi he has created. Pretorius wishes to work with Henry to create a mate for the Monster, with the proposed venture involving Pretorius growing an artificial brain while Henry gathers parts for the mate.

That night, following the sound of a violin playing "Ave Maria," the Monster encounters an old blind hermit who thanks God for sending him a friend. He teaches the monster words like "friend" and "good" and shares a meal with him. Two lost hunters stumble upon the cottage and recognize the Monster. He attacks them and accidentally burns down the cottage as the hunters lead the hermit away.

Henry and Elizabeth, now married, are visited by Pretorius. When Henry expresses his refusal to assist with Pretorius' plans, Pretorius calls in the Monster, who demands Henry's help. Henry again refuses, and Pretorius orders the Monster out, secretly signaling him to kidnap Elizabeth. Pretorius guarantees her safe return upon Henry's participation. Henry returns to his tower laboratory where, despite himself, he grows excited over his work. After being assured of Elizabeth's safety, Henry completes the Bride's body.

A storm rages as final preparations are made to bring the Bride to life. Her bandage-wrapped body is raised through the roof, where electricity is harnessed from lightning to animate her. Henry and Pretorius lower her and, after realizing their success in bringing her to life, remove her bandages and help her to stand.

The Monster comes down the steps after killing Karl on the rooftop and sees his mate. The excited Monster reaches out to her and asks: "Friend?" The Bride, screaming, rejects him. The dejected Monster observes: "She hate me! Like others." As Elizabeth races to Henry's side, the Monster rampages through the laboratory. When Pretorius warns that the Monster's actions are about to destroy them all, the Monster pauses and tells Henry and Elizabeth: "Go! You live! Go!" To Pretorius and the Bride, he says: "You stay. We belong dead." While Henry and Elizabeth flee, the Monster looks at the Bride, sheds a tear, and pulls a lever to trigger the laboratory and tower's destruction.