Abetted by the elderly Dr. Hertz (Thorley Waters) and handyman Hans (Robert Morris), Baron Frankenstein (Peter Cushing) determines that the soul does not immediately leave the body upon death, and can be transplanted from one body to another with a special apparatus he has developed. Hans is in love with Christina (Susan Denberg), the disfigured daughter of a local innkeeper. Christina's father disapproves of their relationship because Hans's father was executed for murder -- an execution Hans witnessed as a young boy. One night, while visiting Christina at the inn, Hans fights with three upper class snobs -- Anton (Peter Blythe), Johann (Derek Folds) and Karl (Barry Warren) -- when they insult her. Later that night, the three snobs sneak back into the inn and assault Christina's father, killing him.
Hans is arrested for the murder. Despite the sterling character references of Dr Hertz and Frankenstein, the testimony of Anton, Johann and Karl persuade the jury. Because Hans will not reveal his whereabouts during the time of the murder -- he was making love with Christina -- he is sentenced to die at the same guillotine that killed his father some twenty years earlier.
Frankenstein sees this as an opportunity to test his new machinery on a human, and he has Dr Hertz arrange to receive Hans's dead body. Christina, unaware that Hans had been sentenced to death, stumbles upon the execution site and sees Hans die. Distraught, she throws herself off a bridge and drowns. Frankenstein and Hertz successfully trap Hans' soul. The authorities bring Christina to Dr Hertz's office. Frankenstein persuades Hertz to trap her soul; once they have healed her injuries and facial disfigurements, they will restore her soul to her body.
The procedure is a success. At first Frankenstein refuses to reveal to Christina who she really he is or allow her to leave Hertz's house, but after a few weeks he takes her to see the guillotine. When Christina sees the device she cries out "Papa!" and faints. Frankenstein's suspicions are proven: both Hans's and Christina's souls are in her body. As Frankenstein devises more experiments, Hans's soul overtakes Christina's and urges her to avenge her father. She dresses up like a promiscuous woman, seduces Anton and Johann and kills them.
Christina scrawls "Hans" in blood next to Johann's name, leading authorities to assume that Hans had sent someone else to the guillotine and had survived himself. They go to Hertz and Frankenstein, assuming their complicity. Frankenstein reveals the truth: Hans's soul is controlling Christina. He then tracks Christina to the woods where she has taken Karl for a picnic. He arrives too late: Christina has killed Karl and is now "speaking" with Hans's severed head which "informs" her that her work is done. Shocked at what she has done, Christina's soul resumes control and rushes to the river bank. Frankenstein promises to help her, but she cannot endure her guilt and throws herself to her second watery death. Frankenstein walks sadly away.