Godzilla versus Destroyah would be the last Godzilla movie to end the series, with Godzilla dieing at the end. This allowed the general public to know that Godzilla died, but he died fighting a monster and saved the world from being destroyed. It is shown at the end that Godzilla's son lives on and continues the Godzilla theme, though this never actually happens and the movies after this are just reboot's to the series, introducing a new Godzilla costume each time and following the first movie. However, the producers had different plans.

Before the idea of Godzilla versus Destroyah, the original movie was meant to be called Godzilla versus The Atomic Monster, which was a completely new monster which was not Destroyah. The cast would be Godzilla, Mothra, Mechagodzilla, Battra, King Ghidorah and 'The Atomic Monster'. This new monster would be a shape-shifting monster that took the form of other monsters and new ones, but the movie also had the other monsters in it too.

The movie starts with Godzilla destroying Japan again, as the movie usually starts out. People are heard screaming and are seen running around the city trying to escape. Godzilla blasts his Atomic Breath at a Japaneese airport, and destroys a plane which took off from the landing strip. His famous roar is heard, lasting longer than usual though, and seems to echo through the entire city. Godzilla looks improved, similar the Godzilla costume in 'Godzilla versus Destroyah'. The army send in fighter jets and planes to stop Godzilla, but they are destroyed in mid air. The planes are seen crashing into cities as people are crushed by them, and it even shows a small boy being crushed by Godzilla's foot. Suddenly, Godzilla starts to become skinnier, and more darker as it is revealed not to be Godzilla, but the 'Atomic Monster'. This monster is a tall, black monster with four arms and spikes pertruding from them. It suddenly starts growing features of other monsters. It has Baragons horn, Ghidorah's wings, Biollante's head, Gigan's chest buzzsaw, Angirus's spikes on its arms, and finally, Godzilla's spikes on it's back. It starts using all the monsters special attacks, and constant lasers and explosions are fired. 

Then, the scene shows a team of scientists who have found one of Mothra's eggs. It is surrounded by scientific equipment and there are military cars and soliders around it. An English speaking scientist says: 'Mothra's egg should hatch soon, when it does, we can begin testing'. We can assume that these people want the offspring of Mothra to hatch so they can find ways of fighting other monsters with it. Whilst the scientists are speaking, a meteor is seen heading to earth. The scientists are seen looking through binoculars and talking in Japaneese, however, the English speaker is talking to an English speaking soldier, saying 'Keep your weapons aimed at that thing, it might be Mothra or something else coming to take it'. As the meteor gets closer, the rock explodes off of the core, as it shatters in mid-air. It is revealed to be Mechagodzilla, as it lands on the beach, cracking the mountains in the distance. Mechagodzilla's design is the same as Kiyru's design in the newer installments, as it begins to unload it's godly amount of weapon's onto the soldiers. Soldiers are seen being shot by Mechagodzilla's lasers and also being disintegrated by it's 'laser breath'. When all the soldiers and scientists are dead, Mechagodzilla aproaches the egg. Mechagodzilla cracks the egg open, seeing the larvae inside fully developed. He then picks up the larvae and it seen throwing it into the mountains as they collapse on it. Then, Mechagodzilla fires rockets at the rubble, burying the larvae under heaps of rock. It is then seen taking off over a forest area.

Then it flashes back to 'The Atomic Monster' who is blasting lasers and shooting buildings. This is the first monster that actually eats people, as it is seen picking groups of people up and shoving them in its mouth. You can actually hear the crunching of bones and their screams inside its mouth. Suddenly, the monster notices Mechagodzilla flying over the city, as it is seen shooting the Atomic Monster in the neck. It screams in pain as blood is seen shooting out of its neck. The Atomic monster then grabs Mechagodzilla's tail and flings him into a building, as the building's rubble falls on top of it. The civilians are seen running past Mechagodzilla's body as it begins to move. Eventually, he manages to get back up, and starts firing missiles at the Atomic Monster. The Atomic Monster is seen grabbing one of Mechagodzilla's missiles and throwing it back, this hits Mechagodzilla's head and destroys it. People are heard screaming and running still, and the army arrive trying to kill the monster, but of course, it doesn't work.

It then finally shows Godzilla, arriving out of the sea and toward the land where The Atomic Monster is walking around, devouring people. Godzilla roars, gaining the monsters attention. The monster recognises Godzilla, and suddenly strange text appears. The Atomic monster roars, as the dialogue at the bottom says : 'You're too late, this city is mine! as the roar continues towards Godzilla. Godzilla then speaks whilst roaring, as the dialogue says: 'I am here to protect this city and stop you from spreading!'. The monsters start having a conversation from their stance points. The dialogue below shows what appeared on the screen:

Atomic Monster: You will never save this city, you are too old. Take another rest.

Godzilla: You are the filth of our kind!

Atomic Monster: Join me, and I will give you the peace and immortality you deserve.

Godzilla: I would rather die than work and serve you.

Godzilla then fires his atomic breath at the monster as it explodes on it's body. The Atomic Monster roars, and fires it's atomic breath back at Godzilla. As it collides with Godzilla, the screen fades out, and shows Mothra flying over the mountain where her offspring was killed by Mechagodzilla.  She lands on the floor and is seen sniffing the rocks where it is under. Then, a human female crying is heard. This is where the movie starts to become creepier and stranger. A female child is heard crying and Mothra has blood around her eyes. She is then seen flying up from her position and going over the crumbled mountain. The movie fades back to Godzilla, getting up from his blast, as more dialogue at the bottom happens.

Godzilla: What are you, and why are you here.

Atomic Monster: I am here to put civilisation to its right purpose.

Godzilla: You should not be here!

Suddenly, it shows Mothra flying over Godzilla's head, straight towards the Atomic Monster. We can assume that Mothra thinks this is the monster that killed her offspring and she is flying fast towards it. Suddenly, an extremely graphic scene happens when the Atomic Monster is seen stretching its mouth wide open, as Mothra flies inside it. She is seen being devoured by the monster as blood comes out the ridges of its teeth and splats on the floor. Godzilla looks on in shock and roars. After the monster has eaten Mothra, more dialogue appears.

Atomic Monster: Would you like the same to happen to you? You are worthless and have no strength to defend this city, give yourself up Gojira, let the pain end.

Godzilla: You are an abomination. I will end you.

Atomic Monster: You will try, though you will not win.

Godzilla then fires his atomic breath at the Atomic Monster, as the spike on the Atomic Monsters head abzorbs it and fires it back. This cripples Godzilla as he falls to the floor. Then, The Atomic Monster starts taunting Godzilla about previous things from movies.

Atomic Monster: You are a coward. You cannot stop me, nobody can. You didn't stop me from killing Angirus, or killing Mechagodzilla. You didnt stop yourself from exploding, the army did. You couldn't defeat the rose that turned into your worst nightmares. I will end you here.

(What is strange, is that Godzilla doesn't start to explode until Godzilla versus Destroyah, which should have been a movie after this) 

Godzilla: No, this is my planet and the people who own it. I inhabited it long before you imbociles, leave!

The Atomic Monster then places it's foot on Godzilla's head, as if it was about to crush Godzilla's skull. Just before it does though, we hear Ghidorah's cackle, as he is seen flying down. Ghidorah lands behind Godzilla, and faces The Atomic Monster. He even has some dialogue.

Ghidorah: You are to leave this to me. You have no right to commit this.

Atomic Monster: No Ghidorah, but you were always a traitor to me.

Ghidorah: Only a battered mutant like you would know that.

Atomic Monster: And what do you purpose I do?

The Atomic Monster is then seen lifting its foot of Godzilla's head, as Godzilla is seen standing shakily moving to the side.

Ghidorah: He is to be preserved for our own sake.

Ghidorah then fires electricity from all three heads at The Atomic Monster, as it is seen falling back into buildings. Ghidorah seems to ignore Godzilla and trudges forward, still shooting at The Atomic Monster. The monster gains enough energy and starts to fight back, Ghidorah bites the horn on the monsters head, and snaps it off. A loud, echo of a crack is heard at this point, and then it focus's on Godzilla's face. He starts to fire his Atomic Breath at the monster along with Ghidorah blasting at it with electricity. The monster starts loosing the features of other monsters, like Baragons horn, one of  its arms, and some of Gigan's chest buzzsaw peices. Eventually the monster falls into a large building, and is paralyzed. Ghidorah starts stamping on the monsters chest as blood comes out of the monster. The Atomic Monster suddenly opens a chest cannon, similar to Destroyah, and fires it. This shoots through Ghidorah, killing him instantly. Godzilla watches Ghidorah die, and roars. The monsters are seen roaring at eachother, though we dont see any dialogue. Godzilla looks angry when he roars and the Atomic Monster has a crooked smile on its face. Godzilla then blasts the monsters head, as it explodes. Chunks of flesh fly into the air as the monster is killed. 

The final scene shows Godzilla looking at Ghidorah's body, as he is still alive.

Ghidorah: I am sorry, I am sorry.

Godzilla: Sorry for what? You have helped me.

Ghidorah: I always hated you, but I had to help.

Godzilla: I'm sorry Ghidorah.

Ghidorah: Please, let me die.

Godzilla looks upset now, as his mouth ridges lower. He looks at the monster Ghidorah assisted him in killing, and suddenly starts to explode like in Godzilla versus Destroyah. Eventually, Godzilla actually explodes, but doesn't destroy the whole world as they claim in Godzilla versus Destroyah. Junior is seen at the end walking over one of Ghidorah's heads to the remains of his father. He roars in sorrow, and then the screen fades. Then, the outro music starts playing, and the roll credits are shown. At the end, it shows some text in Japaneese saying 'Bye Bye Godzilla' in a strange hellish colour. Then the movie ends.

In the movie, it says Battra is cast to appear, though he never acutally appears.