On Christmas Eve in 1955, the adolescent Hellboy is preparing for bed and requests a bedtime story from his father, Professor Bruttenholm (John Hurt). The professor tells Hellboy a legend about war between the humans and the people of the mystical realm. King Balor, leader of the magic elfin race, commissioned the creation of a "Golden Army," 70 times 70 magical mechanical soldiers. Balor received a crown that would allow him (or anyone with royal blood) to command the Army. The Golden Army attacked the humans with no mercy, and eventually Balor became consumed by regret. A truce was called between the warring factors; humans were given control of the cities while Balor's elves would keep to the forests. As a peace offering, Balor shattered his crown and gave one piece to the humans (still keeping two for himself). One of the few who did not agree with the truce was Balor's son, Prince Nuada. The Prince went into exile, vowing to return when his people needed him. And the Golden Army became dormant.

In the present day, a mysterious albino man (Luke Goss) is practicing swordsmanship. It is Prince Nuada, ready to return from exile. He is joined by the monster known as Mr. Wink (Brian Steele) who follows his commands.

A prestigious auction house is selling off several rare artifacts, including the humans' fragment of the Golden crown. Nuada arrives, takes the crown fragment and dispatches several mysterious creatures to dispose of the humans.

At the Bureau for Paranormal Research and Defense, Agent Tom Manning (Jeffery Tambor) has a meeting with Abe Sapien (Doug Jones). Manning is still mad at Hellboy; the B.P.R.D. is still an undercover organization yet Hellboy continues to let himself be seen in public. Abe explains that Hellboy's relationship with Liz Sherman is "tense" at the moment, which may be causing Hellboy's erratic behavior. At that moment, Hellboy (Ron Pearlman) is blasted through the wall of his room; his pyrokinetic girlfriend Liz (Selma Blair) has become extremely angry and used her fire powers to send him flying.

Hellboy's team is called to investigate the incident at the auction house. Manning gives Hellboy a pack of Cuban cigars as a bribe in one last attempt to persuade Hellboy to be discreet in his work.

At the auction house Hellboy & the others learn that there are no survivors from the 70+ guests reported to be there. Abe searches through texts to find what might have caused such an attack. He finds boxes marked with a Royal Seal and uncovers an example of what the boxes might have contained: small, winged creatures known as "tooth fairies" because they feed on calcium. While using his psychic talents to try and find the creatures, Abe brings his hand close to Liz and senses that she is pregnant.

Hellboy and his fellow agents are suddenly swarmed by the ravenous tooth fairies. Liz activates her fire powers in a desperate attempt to burn out the creatures. The resulting battle sends Hellboy outside and in full view of news reporters. The BPRD is officially exposed to the world.

Meanwhile, Prince Nuada and MR. Wink come to speak with King Balor. Balor is content to let the truce between humans stand, and his daughter Nuala (Nuada's twin sister, Anna Walton) is in agreement. But Prince Nuada feels that humans are insatiably greedy and will soon force the mystical creatures into extinction.

Hellboy watches news reports about himself and the other agents on the evening news. Hellboy is delighted by all of it but Liz (secretly taking a pregnancy test) is furious about Hellboy making them public because she hates people "staring at her." Tom Manning tells Hellboy that Washington is sending down a new BPRD agent as a result of Hellboy's latest actions. Hellboy is less than thrilled.

Balor and Nuada continue their argument. Nuada refuses to back down; he will do whatever is necessary to make the magical world safe from humans. Nuada kills his father and takes the second piece of the crown. Nuala flees from her brother with the third and final piece.

Everyone at BPRD is awaiting the arrival of their new agent, Johann Krauss (voice of Seth MacFarlane). Krauss turns out to be a very strange entity; a containment suit proportioned like a man holding pure ectoplasmic energy.

Krauss inspects the remains of one tooth fairy. He injects it with a sample of ectoplasmic energy to temporarily return the creature to life so they might learn more. Krauss translates the creature's speak; it remembers troll languages and other commerce sounds. Johann realizes that the creatures came from the legendary Troll Market, a gathering place for magical creatures. Rumors suggest that the Troll Market might be located under the Brooklyn Bridge so Krauss takes the team to search for it.

Johann Krauss outfits the team with special time-dilation glasses that allow them to see through illusions put out by magical entities. They end up spotting a creature called a "fragglewump" who leads them right to the door of the Troll Market. Upon entering, Hellboy is delighted- he can walk among the Market's creatures and not feel like a freak or outsider.

Abe spots a hooded figure walking away and wearing the same sort of Royal Seal he found with the tooth fairies, so he goes to investigate on his own. The figure is Princess Nuala, who arrives at the Market's library to receive a cylinder hidden by her father. Abe follows her in and she confronts him. Nuala is revealed to have the same sort of psychic powers as Abe. They both learn about one another through hand gestures.

At that moment, Mr. Wink comes in and attacks Nuala. Abe encourages her to flee while Hellboy fights Wink. After an intense fight, Hellboy proves victorious. They speak with Princess Nuala, who explains that she has the last piece of her fathers' crown and the cylinder from the library which contains a map to the location of the Golden Army. Krauss is worried about bringing the princess back to BPRD because of regulations, but Hellboy argues against him.

Prince Nuada arrives soon after, furious at the loss of his companion. He releases a small seed, which Hellboy scoffs at. It suddenly and rapidly grows into a multi-tentacled creature; a forest elemental. Upon seeing the gigantic creature, Hellboy trades in his trademark "Samaritan" pistol for a gigantic six-barreled minigun nicknamed "Big Baby."

During the fight with the elemental, Hellboy saves a human infant from certain doom. But when the fight ends, Hellboy is taunted and jeered by the crowd for bringing danger to a child. The humans call "Hellboy" a freak.

Later on, Liz patches up Hellboy- who doesn't understand the humans' reaction. Liz tells Hellboy that she is leaving to "think." Hellboy automatically assumes that he has doomed their relationship and begs her to stay. Liz asks Hellboy to decide what he really wants- the world's approval or HER approval.

Abe has a conversation with Nuala, who explains that she is connected to her brother in a psychic link and now that Abe has shown her the BPRD location, Nuada knows where she is. Nuala hides the 3rd crown fragment in one of Abe's books.

In the locker room, Hellboy is confronted by Johann Krauss. Krauss wants Hellboy to start following orders, and warns Hellboy that if the 2 had to fight then Krauss would probably win. Hellboy, undaunted, asks why. Johann explains that Hellboy's temper is his worst flaw; he allows it to get out of control and get the best of him. Hellboy, proving Johann's point, smashes the helmet of the containment suit. Krauss' ectoplasmic energy takes control of the locker doors, smashing Hellboy several times before wandering off.

Hellboy meets with Abe, who is in the middle of listening to a collection of popular love songs. Hellboy realizes that Abe has fallen in love with the princess. The two best friends get drunk and begin contemplating their relationships. Abe is on the verge of revealing to Hellboy why Liz has been acting so different lately when Liz storms in on them, furious.

Nuada breaks into the BPRD, steals the map to the Golden Army and abducts Nuala. He also leaves a psychic message to Abe stating that if they bring the 3rd crown piece to the Army's location, he will spare their lives and release Nuala. Nuada finishes by stabbing Hellboy with an enchanted spear.

Despite the best medical efforts, the spearhead cannot be removed from Hellboy's chest (any attempt to pull it out forces the spearhead to move closer to Hellboy's heart). Hellboy, in pain, admits to Liz that she is more important than anything else in his life. Meanwhile, Abe finds the 3rd crown piece in his book.

Analyzing the remains of King Balor's map tells the BPRD that the Golden Army is located in northern Ireland. Liz wants to take Hellboy there to heal him, but Manning & Krauss are willing to let Hellboy die to keep the Golden Army from awakening. Liz berates Johann for his attitude, storming off.

Abe & Liz decide to take Hellboy without approval, desperate to heal their friend. Johann confronts them on their way out and to everyone's surprise he volunteers to help.

In Ireland, the group encounters a goblin who offers to lead them to the Golden Army for "something shiny." The goblin spots the spearhead shining beneath Hellboy's bandages and offers to help remove it if they give him the spearhead as payment.

The goblin brings them before a mysterious winged creature. It is the Angel of Death. The Angel knows Liz and Hellboy (calling him by his true name, Anung Un Rama) and has been waiting for them. The Angel cares not whether Hellboy lives or dies; but Liz begs for Hellboy to live. Despite the Angel's warning that Hellboy's survival will eventually bring about the destruction of Earth (and that Liz will suffer most of all because of that), Liz still asks for Hellboy to live. The Angel removes the spearhead and instructs Liz to give Hellboy a "reason to live." Liz kneels down and tells Hellboy that he is to be a father. Hellboy stands up, fully recovered but awestruck upon hearing Liz' news.

Their goblin guide leads the group to the central chamber of the Golden Army, where Prince Nuada waits with his hostage. Abe gives Nuada the last crown piece in hope of freeing Nuala, but the Prince betrays them and awakens the Golden Army.

Despite a valiant effort by Hellboy and the others, the 4900 Golden soldiers appear unstoppable. Hellboy then comes up with an idea; he challenges Prince Nuada for the right to command the Army. Nuala realizes that Hellboy (or Anung Un Rama) is born of royal blood and thus the challenge must be answered.

Hellboy fights against the prince across the entire chamber, at one point finally gaining the upper hand. But he refuses to take the Prince's life. As they fight, Nuala feels the wounds that Hellboy inflicts upon her brother. Nuada prepares to stab Hellboy in the back, but suddenly collapses from pain in his chest. Nuala is revealed to have stabbed herself in the heart in a final attempt to stop her brother. Abe goes to Nuala's side and confesses his feelings to her before she dies.

With Nuada dead, Hellboy is considered the winner of the challenge by default. He picks up the completed crown and hands it to Liz, who burns it-sending the Golden Army back into hibernation forever.

By this point, Manning and the other BPRD agents have caught up to Hellboy. Manning demands an explanation but instead Hellboy, Abe and Liz all hand in their belts, resigning from the BPRD (Hellboy hesitates only a moment to reclaim his "Samaritan" gun). Manning requests help from Krauss, but Johann merely tells him off and goes to join the others.

Hellboy suggests that he and Liz get a place of their own to raise the new baby. Liz stops him and says "Babies," holding up two fingers- a sign that she is carrying twins. Hellboy can only look on in shock and wonder.

After an ancient truce existing between humankind and the invisible realm of the fantastic is broken, hell on Earth is ready to erupt. A ruthless leader who treads the world above and the one below defies his bloodline and awakens an unstoppable army of creatures. Now, it’s up to the planets toughest, roughest superhero to battle the merciless dictator and his marauders. He may be red. He may be horned. He may be misunderstood. But when you need the job done right, it’s time to call in Hellboy.