CONTAINS SPOILERS FOR ULTIMATE FANTASTIC FOUR
I think the story should be the same as in Ultimate Fantastic Four. Reed Richards should be a geek, who is asked to join The Think Tank, where he meets Johnny and Sue Storm and Victor Van Damn. The Moleman should be a teacher, who is fired because he has been doing illegal experiments creating life. Ben Grimm should then show up years later before their experiemnt and unwhittingly becomes The Thing. Sue is kidnaped by Moleman, Reed is found in the desert, The Thing in Mexico and The Human Torch is France. Wanting to bring the Storm children together, Moleman sets a monster on the city to get Johnny.
Dr. Doom should not be introduced until the sequal.