In the year 2099, Mister Fantastic, the Invisible Woman, the Human Torch and the Thing found themselves in new uniforms and transported to a very different Negative Zone than the one they knew. Returning home, they found the world changed and S.H.I.E.L.D. soldiers chasing after them as laboratory copies of the original Fantastic Four.
During a fight with a repo-man crew named Total Recall, a church dedicated to the worship of the 20th Century’s Thor was destroyed and the FF escaped with an injured Human Torch to an abandoned S.H.I.E.L.D. hideout. They discovered through the repo-men that Stark-Fujikawa claimed them as “experimental subjects,” and so they headed off to the Alchemax building to prove their originality. The four encountered the new century’s Spider-Man, who helped Reed Richards study their own DNA, but due to the advanced technology of the year 2099 the results were inconclusive, leaving their legitimacy in question.
They then decided to break into their old headquarters at Four Freedoms Plaza with the help of their friend, Chimera, who came back with them from the Negative Zone. Though before they could return to the Negative Zone to find a way home, they were attacked by a man named River Styx, the demon brother of Chimera, as well as a group of Shield soldiers. In the course of the battle the Negative Zone door was damaged, causing a leak into the worlds, which collapsed releasing Mindless Ones, who were destroyed at the last minute by the 20th Century’s Doctor Strange, who leapt into the future to warn the denizens of Earth of the approaching end of the world.
A planetoid was headed to Earth, causing the polar ice caps to melt, drowning most of the world’s populace. The Fantastic Four set up headquarters in their old building to try and assist the Earth’s future inhabitants. The Human Torch headed out to investigate the flooding, but was ambushed and captured by the Atlanteans and their leader, Attuma. The Invisible Woman and the Thing rushed to his rescue, getting themselves captured as well, and found themselves caught in the middle of a fight between Attuma and the rightful ruler of Atlantis, the mutant Whisper. After being injected with drugs to turn them against Whisper, the effects wore off, and the three members of the Fantastic Four helped Whisper regain her throne and defeat Attuma.
Back in Nueva York, Reed worked together with the remaining survivors of the flooded city, after he was forced to ask for help by his one-time arch nemesis, the future Doctor Doom. While fleeing the city towards the Savage Land, the only place on Earth free from flooding, a fleet of Atlantean ships attacked the remaining humans. But the human fleet was saved from destruction by the interference of Doom’s Latverian Luftwaffe, and finally by Whisper’s command as the new Atlantean leader to let them be.
The Fantastic Four, along with the last refugees of Earth, finally settled in the Savage Land to rebuild humanity. Their next step was to send out a ship piloted by the Thing, and crewed by Father Jennifer and the mutants December, Twilight and Smith. The ship rocketed off towards Mars until cosmic rays disrupted the ship and it crashed on the alien planet.