When Onslaught was created, because a combination of Professor X's and Magneto's psionic energy released during a battle, Onslaught started to kill many people in New York State. All the Fantastic Four and many Avengers were killed by Onslaught while trying to defeat him. Franklin Richards, the son of the Fantastic Four's Invisible Woman and Mr. Fantastic, was left orphaned after the battle. Franklin's paternal grandfather, Nathaniel Richards, took him to the Xavier's School For Gifted Youngsters, where the X-man Banshee was put in charge to take care of Franklin. While at the school, Franklin met Artie and Leech, two young mutants, like him. In a short time, the three young boys became best friends.
Tana Nile, an alien from the planet Rigel-3, crashed on Earth. Artie, Franklin and Leech found her and took her to their three house in the Danger Room's Bio-Sphere witch was in the school itself. Tana was there hidden from Emma and Banshee, the headmasters of the school. Some time after, they met Howard the Duck, an alien looking like a talking duck.
After Black Tom attacked the school , Franklin Richards subconsciously desired a means of escape. He used his innate mutant powers to summon the swamp-guardian known as the Man-Thing to the school.
Franklin Richards, Leech, Artie Maddicks, Tana Nile, Howard the Duck and the Man-Thing escaped Black Tom by traveling through a portal on a chunk of earth, but found themselves now floating through the Nexus of All Realities.
Tiring of Howard's complaining, Tana Nile tosses him off their 'island' and the Duck falls through one of the doorways populating the Nexus.
Howard lands in Nevernevernarniozbia, a land that appears to be an amalgam of many storybook worlds peopled by fairy tale versions of super-heroes and villains. The rest of the group follow through the same doorway, but are themselves followed by a living shadow called the Dark Hunter.
The group is soon captured by a wicked version of the Scarlet Witch, then are reunited with Howard who has also been captured. Leech negates the powers of his captors, and he and his friends almost escape, but are stopped short by the Dark Hunter. To the shock of Howard and the rest, the Man-Thing speaks.
In the twisted storybook land of Nevernevernarniozbia, Franklin Richards, Leech, Artie Maddicks, Tana Nile, Howard the Duck and the unexpectedly verbal Man-Thing are confronted by the Dark Hunter, who states he is for Franklin. The good witch called Strange arrives to dispell the form of the Dark Hunter, then spirits the group to another fantasy land, this time resembling the works of Dr. Seuss.
When they can't get the hang of speaking in verse, they are arrested and jailed by the Cadence Police. The Dark Hunter finds them in the jail and the group breaks free, but the persuing Hunter kidnaps Artie.
Howard appeals to the Man-Thing to try to teleport them to where they can rescue Artie, despite the fact that that power was one the muck monster exhibited only once before. Still, he tries, and the crew find themselves on Duckworld, where Howard has been worshipped as a mega-celebrity.
While Artie Maddicks is held captive in the shadows of the Dark Hunter, Franklin Richards, Leech, Tana Nile, Howard the Duck and the Man-Thing try to evade mobs of Howard's adoring fans on Duckworld. Reluctantly, Howard agrees to lead the group to his parents' home.
Meanwhile, the Dark Hunter reveals his true nature to Artie, who agrees to aid the shadowy form.
On Duckworld, the crew meets Howard's family and his father explains Howard is a celebrity thanks to video transmissions of his adventures, captured by a Dr. Richards, and sold as entertainment. Howard, however, tells the rest that this sitcom-based family is not his, while a distressed Franklin causes Leech and Man-Thing to vanish. Thinking this Dr. Richards may have answers, Howard and Tana Nile seek him out.
When they arrive with Franklin, they find two-dimensional replicas of Mr. Fantastic and the Invisible Woman, and the boy happily walks off with them while Howard and Tana Nile now find themselves in the company of the Dark Hunter. The shadowy being explains to all that he is the manifestation of Franklin's fear, grief and denial, and that the worlds they have visited, as well as the Man-Thing's unprecedented abilities of speech and teleportation, were all products of the boy's unconscious, created through his mutant powers. They confront Franklin who tries to resist, but finally accepts that his parents are gone.
With Franklin's negative emotions released, the sextet find themselves in the Florida swamp that is the Man-Thing's home.