Hellboy (Ron Perlman), his pyrokinetic girlfriend, Liz (Selma Blair), and aquatic empath, Abe Sapien (Doug Jones), face their biggest battle when an underworld prince (Luke Goss) plans to reclaim Earth for his magical kindred. Tired of living in the shadow of humans, Prince Nuada tries to awaken an ancient army of killing machines to clear the way for fantasy creatures to roam free. Only Hellboy can stop the dark prince and prevent humanity's annihilation.

Marnie and her kids get a big shock when they follow grandma home to Halloweentown - and find out they come from a family of witches. The town is the only place where supernatural beings can lead a 'normal' life, but trouble is looming, and on her 13th birthday Marnie not only finds she is a witch, but that she and her family are involved in a fight against the evil that is threatening to take over the world.

Grandmother Aggie (Debbie Reynolds) sweeps Marnie (Kimberly J. Brown) and Sophie (Emily Roeske) off to Halloweentown to investigate a series of strange occurrences. When they arrive, the vibrant community seems to have lost its magic. It isn't long before Aggie discovers that her spell book is stolen, and the trio must find it. They discover that an angry warlock has taken the book and plans to permanently turn every human into whatever costume they are wearing on Halloween.

Marnie organises a student exchange programme between her mortal school and the Halloweentown High. The first students to participate in this programme are a witch, a warlock, a troll and an ogre.

At the end of World War II, the Nazis attempt to open a portal to a paranormal dimension in order to defeat the Allies, but are only able to summon a baby demon who is rescued by Allied forces and dubbed "Hellboy" (Ron Perlman). Sixty years later, Hellboy serves as an agent in the Bureau of Paranormal Research and Defense, where he, aided by Abe Sapien (Doug Jones), a merman with psychic powers, and Liz Sherman (Selma Blair), a woman with pyrokinesis, protects America against dark forces.