In the age of dinosaurs, Reed warns everyone not to touch anything so they can avoid changing the future. Ben looks guiltily at the Tyrannosaurus Rex he was forced to knock out. He also warns them not to mess with the temporal stasis devices on their arms that allow them to exist in the past. They are unaware that a small robot spider-drone has attached itself to the Fantasticar. Reed tries to figure out how the dinosaurs were wiped out, and Johnny points out the giant meteor heading toward them. They quickly leave as the meteor strikes.
The team travels back to the present, unaware that the spider-drone has detached itself and slipped away into the timestream. They hit time turbulence and materialize over New York City... where the Statue of Liberty has been replaced by a statue of Dr. Doom. The Baxter Building has been transformed as well and a hologram of Doom's mask is suspended over it. Robot patrol helicopters arrive and order them to stand down. Reed takes evasive maneuvers as the robots open fire on them. Ben jettisons the time travel module to give themselves the maneuverability they need to keep ahead of the robots. Johnny feeds his nova blast into the engines, allowing them to get clear long enough for Susan to render them invisible.
The team takes to the streets to find out what's going on. When a homeless person sees them, she screams and runs away. Reed explains that they've returned to the exact point that they left, and Ben wonders if something he did in the past might have lead to the current present. When he explains that he clobbered a dinosaur, Reed assures him that it couldn't have changed the past. As they discover banners for Doom around, a patrol of Doom’s soldiers arrives. Susan renders them invisible and Reed prepares to leave with Susan to find Doom. He discovers that Johnny has gone to get Doom-accino. Once Johnny returns, Reed has Johnny and Ben go to get the module from the river and warns them to keep their temporal stasis devices on so they remain anchored to reality.
Reed and Susan go to the Latverian Embassy, and Reed determines that they don't exist in this reality. Meanwhile, Johnny and Ben arrive at the river and Ben steals some equipment from Doom-Mart. However, they can only watch as a helicopter arrives and recovers the module. Two gigantic Doombots arrive to attack them.
In the embassy, Dr. Doom is waiting for Reed and Susan. He removes his mask to reveal an unscarred human visage, and seals the room. Reed demands an explanation and Doom explains that he avoided doing something this time. Doombots bring in the captive Johnny and Ben, and Doom explains that he had forewarning of their powers. He offers to let them live as long as they us their powers at his command and kneel to him. Reed refuses and Doom explains that his offer wasn't for him. He has the spider-drone destroy Reed's stasis device. As he disappears from reality, he tells the others to go back to the beginning. Doom then repeats his offer to the others. Susan frees her teammates with a force shield and attacks Doom. Ben warns that they have to go and carries her out when she refuses. He leaps out of the building and Susan flies them away on a force field.
As they escape into the city, Susan figures she can use the time module to go back ten minutes and save Reed. They attack Doom's soldiers as they finish recovering the module, hook it up to the Fantasticar, but realize that they don't know how to use it. More giant Doombots arrive as they manage to get H.E.R.B.I.E. online. However, he warns them that they can't go back in time and meet themselves. Susan tells H.E.R.B.I.E. to take them anywhere and he engages the time module.
The team discovers that they've now in a frozen tundra. Two cavemen gather around a flaming Johnny but are unable to provide any help. Susan realizes that Reed wanted them to go back to the day they got their powers, where Doom stopped them. H.E.R.B.I.E. insists that they can't see themselves, and Susan gets an idea.
On the day that the team made their fateful voyage, Reed addresses the reporters and then goes to his lab. He finds his three teammates from the future waiting for him. He faints but soon recovers and accepts their explanation. Reed realizes that Doom won't sabotage the flight, which will mean they never get their powers. Johnny sports the spider-drone as it goes to find Doom and tell him what he needs to do. The past-Ben arrives and Reed quickly covers while Susan renders her teammates invisible. They slip away and Susan and Johnny go after the robot while Ben stays to make sure the past-Reed gets on the spaceship.
The spider-drone tries to find Doom while Johnny and Susan enter the cafeteria. The past-Johnny spots them through a glass pane and Johnny is forced to impersonate his past-self's reflection to avoid giving them away. It works and past-Johnny leaves.
Ben calls past-Reed over, and he realizes that the flight is what transforms Ben into a monster. Ben assures him that he's okay with his condition and has saved the world, and past-Reed promises to try and find a cure.
Doom is in his laboratory when the drone starts to tell him. Johnny arrives and stalls while Susan renders the spider-drone invisible. It tries to escape and Susan catches up to it outside. She knocks off one arm but it flies away before she can stop it
The past-Fantastic Four suit up and prepare to depart. Ben watches from the shadows as past-Reed glances once at him. The spider-drone tries to disable the shuttle to prevent the flight and Ben and Susan attack it, and then duck out of sight before the technicians can see them on the security cameras. As Reed prepares to launch, he sees his future teammates battle the spider-drone. He delays the countdown until Susan can knock the spider-drone beneath the rockets. The blast destroys the robot and the shuttle departs as planned.
As the team returns to the present, Reed returns to existence as time is restored. He doesn't remember anything. However, the others discover that Johnny made one small change to the timeline. New Yorkers are now worshipping a Statue of Liberty that looks just like him. Susan orders them to engage the time travel module one more time...