Uatu the Watcher explains to the readers that there exist many realities. In each alternate reality, there is a divergence from what what has happened and what could have happened.
The Watcher focuses on an alternate reality in which Spider-Man attempts to join the Fantastic Four as a solution to his money problems. Originally, Spider-Man is turned down by the group, but in this alternate reality they allow Spider-Man to join, causing the birth of the Fantastic Five.
With Spider-Man on the team, his association with the Fantastic Four grants him acceptance from the population unlike his mainstream counterpart, who is labeled a menace by the Daily Bugle.
The Fantastic Five take on a number of villains, including the Vulture and the Red Ghost and his Super-Apes. While Mr. Fantastic, Thing, Human Torch and Spider-Man go on these adventures, the Invisible Girl often stays behind to monitor things from base.
Sue is eventually seduced into meeting Namor the Sub-Mariner, who is under the control of the Puppet Master to get revenge on the Fantastic Five.