During Christmas 1955, a young Hellboy is told a bedtime story by his adoptive father, Trevor Bruttenholm, about an ancient war between humans and magical creatures. A goblin blacksmith offers to Balor, king of the elves, to build him an indestructible mechanical army. Encouraged by his son Prince Nuada, Balor accepts. The Golden Army devastates humanity. Regretting his actions, Balor forms a truce with the humans. The crown to command the Golden Army, which can only be worn by one of royal blood, is split into three pieces. Nuada, disagreeing with the truce, leaves in exile. In the present, a year after Hellboy foiled the evil sorcerer Rasputin's plans to summon the demonic entities known as Ogdru Jahad and enact Armageddon, Nuada returns and begins gathering the pieces of the crown. He collects the first piece from an auction by unleashing tooth fairies that eat the crowd, and then kills his father for the second piece. His twin sister Princess Nuala escapes with the final piece.
In the Bureau for Paranormal Research and Defense (B.P.R.D.), a restless Hellboy wrestles with his relationship with Liz and with the secrecy that surrounds their work. As he investigates the auction slaughter, Hellboy allows himself to be exposed to the public eye. Amid the chaos, Abe Sapien discovers that Liz is pregnant, though she insists on keeping the news between them. The mood shifts from awe to tension as the team realizes the stakes are higher than ever.
Tom Manning’s superiors decide to rein Hellboy in and bring in Johann Krauss, the ectoplasmic medium who will take command of the mission from within. With Krauss at the helm, the team tracks the tooth fairies to a hidden troll market beneath the Brooklyn Bridge. Abe finds Nuala, who has obtained a map that points toward the Golden Army, and he is drawn to her as much by destiny as by attraction. Hellboy confronts Nuada’s allies, killing Wink and destroying a summoned forest god, a clash that forces Nuada to confront the humanity he’s fought against for so long. Throughout the conflict, Nuada’s bond with his sister grows complicated; their shared wounds and telepathic link reveal the depth of their family ties. Nuala is placed under the protection of the B.P.R.D., while Nuada resumes his pursuit.
Nuada traces his sister to the agency’s headquarters through their magical bond, a bond that also makes their pain and thoughts cross paths. Nuala manages to hide the final piece, but Nuada locates her and a fierce battle erupts between him and Hellboy. In the struggle, Nuada wounds Hellboy with a spear and abducts Nuala, bargaining for the crown piece by promising her return. Unable to remove the spear shard from his chest, Liz and Abe decide to take Hellboy to the Golden Army’s resting place at the Giant’s Causeway in Northern Ireland, where they hope a solution awaits. Krauss accompanies them, revealing his own heartbreak over the loss of his wife in an accident that cost him his body.
The journey leads them to Bethmoora’s goblin master blacksmith, who escorts them to the Angel of Death to retrieve the spear shard. The Angel warns of the cost— Hellboy’s life could doom humanity if he continues to live—but Liz pleads for mercy, and the Angel removes the shard from his chest. She tells Hellboy that he will have a child and that purpose gives him a reason to live. With renewed resolve, Hellboy returns to the mission.
The goblin guide leads them to the resting place of the Golden Army, where Nuada awaits with the crown piece. Abe hands over the final piece and Nuada’s awakened army roars to life. Hellboy steps forward to challenge Nuada for command of the Golden Army. Because Hellboy is part of Hell’s royal lineage, Nuada must accept the duel. Hellboy defeats Nuada and spares his life, but when Nuada makes a last attempt to stab him, Nuala sacrifices herself to stop him. The dying Nuada tells Hellboy that he may have to decide between humanity and the magical beings who share the world. Abe mediumsically shares his feelings with Nuala before she dies, while Liz uses her pyrokinesis to melt the crown, effectively deactivating the Golden Army.
With the threat gone, Hellboy, Liz, Abe, and Krauss resign from the B.P.R.D. and begin to contemplate a future that includes Liz’s pregnancy and Hellboy’s own evolving identity. The final image is intimate and hopeful: Liz raises two fingers in a playful gesture, a quiet smile crossing Hellboy’s face as they imagine what lies ahead.
