It was already known that the Red Skull's daughter Sin would be one of the primary antagonists of the series, and that an old enemy of Thor's father Odin would resurface to cause havoc across the world.
Fraction has now revealed the true identity of the main villain of Fear Itself, as well as how the storyline will begin.
"The Red Skull discovers that Odin isn't the All-father, and frees the true All-father from his prison," Fraction explained to Newsarama. "He transforms the Red Skull into a god for her troubles and they set about waging a war of fear and terror on the world.
"They want nothing more than to make us afraid because the more afraid we are, the worse we are to each other, the stronger they become."
The writer said that the story came about because Marvel editor Tom Brevoort wanted a powerful story involving both Captain America and Thor in order to tie in with the release of this year's two Marvel Studios films.
"You've got Captain America's worst nightmare, which is a Red Skull more powerful than even the original Red Skull even imagined, while he is on desk duty," Fraction added. "You've got Thor's worst nightmare which is everything he knows probably isn't true."
The writer also admitted that he has been dropping hints for the past year in Thor about Odin's true past, noting that a number of things Odin had been saying in the title "don't play right with people".
Fear Itself #1 is due in shops on April 6.