In the year 2099, Mister Fantastic, Invisible Woman, Human Torch, and Thing find themselves in new uniforms and transported to a very different Negative Zone than the one they knew.
During a fight with a repo-man crew named Total Recall, a church dedicated to the worship of the 22nd century’s Thor is destroyed and the FF escape with an injured Human Torch to an abandoned S.H.I.E.L.D.
Before they can return to the Negative Zone to find a way home, they are attacked by a man named River Styx, the demon brother of Chimera, as well as a group of S.H.I.E.L.D.
While fleeing the city towards the Savage Land, the only place on Earth free from flooding, a fleet of Atlantean ships attacks the remaining humans.
The human fleet is saved from destruction by the interference of Doom’s Latverian Luftwaffe, and finally by Whisper, as she asserts her newfound control.
Back on Earth, Johnny and Susan despair as Reed drives himself to exhaustion to establish a technological infrastructure for the remaining humans.
Later in the Marvel 2099 reality of Earth-96943, it is shown that this Fantastic Four team were clones created by Uatu the Watcher to help 2099 humanity which is in danger of extinction.
Some of the highlights of their careers including becoming official Avengers, removing a barrier to space exploration and establishing a peace treaty with Atlanteans.