In 1944, with the help of Russian mystic Grigori Rasputin, the Nazis build a dimensional portal off the coast of Scotland and intend to free the Ogdru Jahad to aid them in defeating the Allies. Rasputin opens the portal with the aid of his disciples, Ilsa von Haupstein and Obersturmbannführer Karl Ruprecht Kroenen. An Allied team destroys the portal, guided by a young scientist named Trevor Bruttenholm (colloquially known as "Broom"). The German team is killed and the portal is destroyed, in the process absorbing Rasputin, while Haupstein and Kroenen escape. The Allied team discovers that an infant demon with a right hand of stone has come through the portal; they dub him "Hellboy" and Bruttenholm adopts him.
60 years later, the eternally youthful Kroenen and Haupstein resurrect Rasputin. FBI agent John Myers is transferred to the Bureau for Paranormal Research and Defense (BPRD) at the request of Bruttenholm, where he meets the adult Hellboy and a psychic, amphibious humanoid named Abe Sapien. Hellboy is sent to investigate an incident at a Museum and battles a creature named Samael. After defeating it, Hellboy visits former BPRD member Liz Sherman at a mental hospital that she committed herself to due to her unstable pyrokinetic abilities. Abe learns that Samael was resurrected by Rasputin, who has imbued Samael with the power to reincarnate and split his essence, causing two of the creature's eggs to hatch and mature each time one dies. Abe also learns that Bruttenholm is dying.
Concluding the eggs are in the sewer, Hellboy, Abe and several FBI agents go down to destroy them. Abe is injured while looking for the eggs, while Kroenen kills most of the agents. Kroenen, whose mutilated body is run by mechanical parts, shuts himself down, pretending to be defeated, and is brought to the bureau. FBI Director Tom Manning is angered by Hellboy's recklessness. Myers takes Liz out for coffee and to talk. Hellboy, jealous, covertly follows them, leaving the bureau unguarded. Kroenen reanimates himself and Rasputin appears at the bureau, confronting Bruttenholm. Rasputin offers him a vision of the future, showing Hellboy is the agent that will destroy the world. However, Bruttenholm tells Rasputin he will always see Hellboy as his son. Rasputin, respecting Bruttenholm for raising Hellboy, directs a quick execution by Kroenen. Bruttenholm dies holding a rosary.
Manning takes over the BPRD and locates Rasputin's mausoleum in an old cemetery outside Moscow, Russia. A team led by Manning and Hellboy enters the mausoleum, but swiftly becomes separated. Hellboy and Manning find their way to Kroenen's lair and kill him. Hellboy reunites with Liz and Myers at Samael's new nest, but the creatures overwhelm them. Liz uses her pyrokinetic powers to incinerate the creatures and their eggs. Hellboy, Liz and Myers lose consciousness and are captured by Rasputin and Haupstein. Rasputin sucks Liz's soul out of her body, then tells Hellboy to release the Ogdru Jahad in return for her soul. Hellboy awakens his true power as Anung un Rama, causing his horns to regrow, and begins to release the Ogdru Jahad. Myers breaks out of his restraints, subdues Haupstein, and reminds Hellboy that he can defy his destiny, throwing him Bruttenholm's rosary. Remembering his true self and what Bruttenholm brought him up to be, Hellboy breaks off his horns, reseals the Ogdru Jahad and defeats Rasputin by stabbing him with one of his broken-off horns.
However, Rasputin has been possessed by the Behemoth, a spawn of the Ogdru Jahad which bursts out of his body, grows to enormous size, and destroys him and Haupstein. Hellboy allows himself to be swallowed by the beast, then detonates a belt of hand grenades and destroys it from the inside. He whispers something in Liz's ear and she is revived. When she asks how her soul was returned, Hellboy replies that he said "Hey, you on the other side, let her go, because for... for her I'll cross over, and then you'll be sorry." Liz and Hellboy share a kiss.
Ron Perlman as Hellboy
John Hurt as Trevor Bruttenholm
Kevin Trainor as Young Trevor Bruttenholm
Selma Blair as Liz Sherman
Millie Wilkie as Young Liz Sherman
Rupert Evans as John "Johnny" Myers
Karel Roden as Grigori Rasputin
Jeffrey Tambor as Tom Manning
Doug Jones as Abe Sapien
David Hyde Pierce as the voice of Abe Sapien (uncredited)
Brian Steele as Samael
Ladislav Beran as Karl Ruprecht Kroenen
Bridget Hodson as Ilsa Haupstein
Corey Johnson as Agent Clay
Brian Caspe as Agent Lime
James Babson as Agent Moss
Stephen Fisher as Agent Quarry
William Hoyland as General Klaus Von Krupt
Angus MacInnes as Sergeant Whitman
Jim Howick as Corporal Matlin
based on the Dark Horse Comics graphic novel Hellboy: Seed of Destruction by Mike Mignola
followed by a sequel, Hellboy II: The Golden Army, released on July 11, 2008 by Universal Pictures, and a reboot, released on April 12, 2019 by Lionsgate.