Fantastic Four is the first movie in the Marvel Feature Animations line.
On a space station far above Earth, the soon-to-be Fantastic Four attempt to perform repairs. Johnny Storm, their mechanic, is doing a spacewalk to recover a piece of broken machinery, but is detached from the station by an asteroid pushing him away. The other three board a manouverable escape pod to attempt to catch him, but end up plummeting to Earth instead.
Johnny is first to land, and finds himself on fire. At first, he is panicked, attempting to put it out. Then he realises it isn't causing him any pain, or damaging him, and he allows the crashing of the escape pod to distract him. Reed's body is strewn out across the wreckage, limbs in every direction. The other two, meanwhile, have disappeared. Susan's gasp draws Johnny's attention to her, and he realises she's become invisible. Reed wakes up next, barely able to stand on his body, but quickly figuring out that he can control it with his mind - as the other two did when he commanded them to.
They question Ben's disappearance, and he shows himself, revealing that he's been listening the entire time and cannot change back from the new orange rocky form he's gained. He lashes out, thinking he'll never have a normal life again. It takes the future superheroes' combined efforts to stop him. With him defeated, the four travel back to their laboratory and home at the Baxter Building. There, they find that the space station has come crashing down to Earth in chunks, a piece of which landing in the nation of Latveria and injuring the country's king, Victor Von Doom, disfiguring him for life. Worse, they find that their connection has been discovered and Doom is seeking vengeance.
He reveals to them that he has been doing research on Earth undergrounds via a video conference and that there lives an otherwise undiscovered species of monsters under New York. He then proceeds to activate emergency procedures at his mine, that reveal an entrance for the monsters to come out of. They are led by the Mole Man, a short old man who has been living underground his entire life. The four fend multiple monsters off before going underground to confront the Mole Man directly. They agree to form a team - the Fantastic Four.
They easily capture him and bring him to a rehabilitation center to adjust him to the surface. However, things are made worse as an external force is attracted to the crash, a Skrull ship. They disguise themselves as the Fantastic Four in order to investigate humanity. Doom attempts to provoke them to attack their human counterparts, but fails when Reed utilises diplomacy to stop them. Terrorist Kl'rt, however, decides to claim Earth as ground for his militant organization and invades.
Kl'rt's invasion is thwarted whenever the Mole Man makes an unexpected alliance with the Fantastic Four. A battle rages between the monsters and the skrulls, with the former emerging victorious. Meanwhile, the Fantastic Four themselves face Kl'rt one-on-one, dealing with his ability to mimic their powers. It is revealed that Doom, too, has had to deal with the fighters in Latveria, which has been ravaged.
The Fantastic Four, deciding to confront Doom while his country's defenses are down, travel there. Failing to convince him not to fight them anymore, they deal first with an entourage of Doombots, then Doom himself. They emerge victorious and are celebrated as heroes world-wide.
The movie ends by panning up to space, then the camera fixates on a silver figure flying past. He approaches a humongous purple-and-blue clad person, telling him that he's found a planet suitable for devouring.