In the Christmas of 1955, a young Hellboy learns a cautionary tale from his adoptive father, Trevor Broom, about an age-old conflict between mankind and magical beings driven by human greed. After years of strife and the magical creatures' defeat, the goblin blacksmiths' master proposes crafting an indestructible golden mechanical army for King Balor, the one-armed elf king. Spurred by his ambitious son, Prince Nuada, Balor commands the creation of this formidable Golden Army, while also forging a magical crown that can control it, but only by someone of royal lineage—if the right to control is unchallenged.
As time passes, humans strike again, but the Golden Army ruthlessly decimates their forces. Balor, saddened by the bloodshed, arranges a truce, ensuring that mankind retains its cities while magical beings preserve their forests. Discontent with the truce, Nuada exiles himself, and to prevent the army's resurgence, the crown is shattered into three pieces: one claimed by humans and two retained by the elves.
Now in the present day, Nuada reignites hostilities against humanity. He retrieves the crown's first piece from a chaotic auction, slaughtering everyone present by unleashing tooth fairies and ultimately killing his father for the second piece. Meanwhile, his twin sister, Princess Nuala, escapes with the last piece of the crown.
During this turmoil, Hellboy finds himself at odds with his girlfriend Liz, struggling to accept the undercover nature of their organization, the B.P.R.D. When investigating the auction massacre, Hellboy inadvertently reveals himself to the world. In the midst of the chaos, Abe Sapien discovers that Liz is pregnant, intensifying the existing tensions within the Bureau. Angered by Hellboy’s public exposure, the Bureau sends in a new agent, the ectoplasmic medium Johann Krauss, to take command. Together, they track the tooth fairies to the hidden troll market beneath the Brooklyn Bridge for crucial clues.
Krauss possesses a unique ability to exert control over living or mechanical beings through an ectoplasmic substance he can release. In this bustling marketplace, Abe encounters Nuala, who holds a map to the Golden Army, and quickly falls for her. After a violent clash with Nuada's ally, the troll Wink, and a fierce elemental forest spirit, Hellboy emerges victorious, but his actions lead him to question his allegiance as he confers with Nuada, who challenges him on whether it is just to defend humans despite being viewed as a monster himself.
Using a magical link, Nuada tracks down his sister to the B.P.R.D. base, causing them to share pain and thoughts. Sensing his imminent arrival, Nuala destroys the map and conceals the crown's final piece within one of Abe’s books. The true map, however, remains with the canister that Nuala disposes of. As Nuada kidnaps his sister, he severely injures Hellboy with a spear, compelling Abe to deliver the crown piece to save his friend and reunite with Nuala.
With no means to extract the spear from Hellboy, Liz, Abe, and Krauss journey to the mystical Giant's Causeway in Northern Ireland to discover the Golden Army's resting place. They meet a goblin who brings them before the Angel of Death, who has awaited their presence. Though warned that Hellboy may be the harbinger of humanity’s doom, Liz pleads for his life. The Angel extracts the spear from Hellboy’s chest, advising Liz to give him a reason to live. Overwhelmed with hope, she reveals that he is going to be a father, prompting Hellboy's recovery.
Their journey leads them to the Golden Army's hideout, where Nuada awaits. In a tense exchange for Nuala, Abe sacrifices the last crown piece. The crown is reforged, reviving the Golden Army, and the relentless soldiers are unleashed against the team. In a desperate bid for control, Hellboy challenges Nuada, who is compelled to accept given Hellboy's royal lineage. After a fierce battle, Hellboy bests Nuada and spares him, yet Nuada attempts to strike Hellboy down. In a tragic turn of events, Nuala takes her life to prevent her brother from further destruction. With her death, Nuada also succumbs, warning Hellboy of a perilous choice between the fate of humanity or the magical races.
As Nuala dies, Abe confesses his love for her through their shared psychic bond. Liz makes the ultimate choice to melt the crown, ceasing the Golden Army's rampage. As the team departs the underground lair, Tom Manning scolds them for their actions. Ultimately, Hellboy, Liz, and Abe decide to distance themselves from the B.P.R.D., with Hellboy reflecting on his newfound future with Liz, who astounds him by revealing she is not just pregnant, but expecting twins.
