Hellboy: Darkness Calls is a comic book limited series created by Mike Mignola and published by American company Dark Horse Comics. Parts of the story arc were adapted for the 2019 Hellboy reboot directed by Neil Marshall.

In Darkness Calls, several plotlines and characters from earlier stories converge.

In a tomb near Lucca, Italy, Igor Bromhead (last seen in Hellboy: Box Full of Evil) summons the witch-goddess Hecate to a catacomb using runes written in blood. She demands to see the lizard body with which the devil Astaroth had cursed him and he obliges. Before she can destroy him he surprises her by invoking her secret name: Ilsa Haupstein, since her resurrection in Hellboy: Wake the Devil. Bromhead reveals the bones of Haupstein's lover and Hecate's son, the vampire Vladimir Giurescu, from which Bromhead has magically wrung the information which gives him full power over the horrified goddess.

Back in England, three witches meet among standing stones; they have recovered the horns Hellboy broke from his skull during Hellboy: Wake the Devil and carved a bust of him from one of them. Hellboy wakes in the house of Harry Middleton, an old friend of his and of his adoptive father Trevor Bruttenholm. Under the witches' (and the carved horn's) influence, Hellboy decides to go for a walk, but not before accepting a vintage pistol and holster from Middleton as a gift. On his walk into the woods he is followed by a troop of cats and spied upon from the trees by a haggard specter with copper coins for eyes. Hellboy encounters two odd men and a woman who see him and cut short their rendition of the evocative "Mister Stormalong" sea shanty, whose monster-hunting folk hero they identify with Hellboy, and whose verses we have been hearing over several pages of captions. They inform Hellboy that they have reached the spot where corrupt 17th-century witchfinder Henry Hood hung three witches, "their ladies", who cursed him with torture and undeath (he is the coin-eyed specter we have seen). After hearing the hanging scene reenacted, the trio rush off to find the burial site of the three hanged witches, whose doting animal familiars they reveal themselves to be: while Hellboy finds himself immobilized (by the spell being cast on his horn) they begin to assume the shapes of a frog, a raven and a cat, resurrecting their former mistresses with a potion poured on their gravesite, and promising Hellboy a gathering of witches (both alive and dead) "like none before in the history of the world" telling Hellboy: "They gather for you!!"

The three witches with the carved horn thank the night and its associated powers for binding Hellboy and for resurrecting their three dead sister witches, executed by Henry Hood but now flying about a shocked Hellboy. The three greet their dead mistresses happily but Henry Hood bursts upon them transfixing two of them with the blue unearthly fire of his cutlass. It also wounds the half-demon Hellboy, who he attacks for his hellish parentage, leaving Hellboy reluctantly to be rescued by the third witch and her raven familiar who carry Hellboy off amid a flock of undead witches "to the sabbath at Leeds" until he shoots her with Harry Middleton's pistol and, dropped, plummets from the sky. He has not escaped, however, as he crashes through the roof of a disused, cobwebbed church and finds it filled with live witches who await him, having summoned him there using his carved horn.

For a cautious, inquisitive Hellboy, they recount the scene between Bromhead and Hecate, filling in relevant history from Hellboy: Wake the Devil and showing a triumphant Bromhead removing Ilsa Haupstein's wailing corpse from the Iron Maiden in which she had become Hecate, and bricking it into an alcove with Giurescu's still-amorous skeleton, there to wait "till Doomsday." Bromhead had then tried futilely and disastrously to become King of the Witches by drawing down lunar powers beyond his strength. They tell Hellboy that as the son of a human witch and of the demon ruling the witches of Lancashire and Abbotsbury (and East Bromwich, Faversham and Berkswell), they have selected him as their king. Hellboy angrily refuses them, declares himself at war with them, and begins to make his way out of the church. The carved horn shatters. Panic-stricken, the witches cast about for a plan, when Koku, a diminutive servant of Hellboy's old enemy Baba Yaga, appears and conveys his mistress' offer to take Hellboy off their hands if they (who unlike the Baba Yaga still live in the real world) "offer" him to her. The witches agree, and Hellboy steps out of the church into the middle of a vast and empty wintry expanse through which an army of armed and fur-clad skeletons approach. Amidst the thicket of impaled lantern skulls in which she keeps her power, we see the Baba Yaga promising to take Hellboy's eye (in return for the one of hers he'd shot out decades before in "The Baba Yaga") and (as the arriving army reports to Hellboy) also his life.

As the witches debate who will rule them if not Hecate or Hellboy, Gruagach makes his presence known and offers the position of leadership to a witch the others fear greatly enough even after they poisoned and dismembered her long ago. Meanwhile, in the snowy plain "beyond the thrice-nine lands in the thrice-tenth kingdom" the Baba Yaga's army attacks Hellboy, who fights for a while and then runs into a wood. Giant wolves rush from the wood to attack the Baba Yaga's soldiers, and a giant white wolf guides Hellboy into the woods to the campfire of his master, the Leshii. Hellboy bores the Leshii, who is nonetheless happy to save Hellboy in order to spite the Baba Yaga. Before departing in the form of a giant horned bear, the Leshii warns Hellboy to stay in the woods only for one night. He asks Perun, the Russian storm-god, to destroy the army, which is buried in snow, as Hellboy finds them when, just before daybreak, he is chased from the woods by the Leshii's wolves. Thwarted, the Baba Yaga flies in her mortar and pestle to the castle of Koschei the Deathless, who broods, cobwebbed on his throne, demanding that if he helps her, she must give him the gift of death. She promises to set him free from life in return for Hellboy's head. Meanwhile, Hellboy finds his way through a winter storm to a small house where he resists a brief attack from, and then makes friends with, the house's guardian spirit or Domovoi. The Domovoi tells him that Perun is hiding him from the Baba Yaga and from Koschei using the storm weather, but that Koschei cannot be killed as his soul is inside an egg inside a duck inside a rabbit inside a goat which the Baba Yaga has hidden. Meanwhile, the Baba Yaga finds Perun (whom we have just seen as a spear-armed horseman riding above stormclouds) drawing lightning branches with a stick in the mud of a riverbank, a mud-caked and naked old man. Her soldiers dispatch him with arrows as she tells him she will tolerate no other Russian gods than herself.

A bird grieves over Perun's body, meanwhile somewhere in England, blood wells over the lintel of a hilltop church, flowing from two murdered monks. A hole in the floor before the altar leads to an ancient cavern where the Gruagach and two elfin servants approach a well with a giant iron lid. When Gruagach rings on the lid with his hammer, a giant appears who puts on spectacles to read the letter Gruagach hands him - from the giant's masters, the witches of Britain - and then begins to weep at what he must do. He raises the lid and climbs down to get his prisoner for the Gruagach. With Perun dead, meanwhile, the storm outside Hellboy's cottage has failed, and Koschei kicks in the door. The two fight as Koschei explains his intentions and motives, and the Domovoi wails over his broken furniture. Hellboy impales Koschei and beheads him but Koschei merely reattaches his head. At that moment Vasilisa, appearing at the cottage's door, subdues Koschei with light from the skull she received from Baba Yaga in her legend. Hellboy pins Koschei to the floor with his own sword and they run. Kosschei ignores the Domovoi's goading, extricates himself, and takes out an arrow from his pack. Vasilisa explains to Hellboy the story of her magic doll and her time with the Baba Yaga, and shows Hellboy the tunnel back to the real world, before falling to the first of Koschei's arrows, which also pepper Hellboy as Koschei rides on them. Dying, Vasilisa gives Hellboy the wooden comb and blue handkerchief her doll had given her ("When I was old and grey and dying in my bed," she says) and then becomes her doll, still pierced by Koschei's arrow. Hellboy confronts the now-arrived Koschei.