My first rework of the films would be Planet of the Monsters. However, I would do what Star Wars Rogue One had done. Instead of a small flashback of the Kaiju War, I would like to expand on it using both materials from the novels that promoted Planet of the Monsters and City on the Edge of Battle. The original plot of Planet of Monsters will be moved to the second film.
Therefore, the title will be Godzilla: Monster Apocalypse
First off would be the characters. Haruo will not yet be the main character but instead I will pass that to his parents, Akira and Haruka Sakaki. Other characters will be shifted to minor roles but the characters that stay are Unberto Mori, Belu-be, Metphies, Dr Martin and Daichi Tani, Yuko's grandfather.
The story is like I said before. There won't be Planet of the Monsters yet but will focus on the Kaiju War.
The opening scene of Monster Apocalypse will take place in Manhattan, 1999. A Boeing 767 was flying towards the island where the people there are either driving, chatting any anything else. A young couple along with their children were on the plane were awaiting their plane to land until suddenly, either the father or mother noticed a silhouetted figure within the clouds and it was getting closer until he/she reacted in horror. At the ground below, people looked up to the sky and saw the Boeing 767 now in flames crashed into the ocean. Then, it happened. Kamacuras exited the skies and attack Manhattan. Police tried to shoot it but had no effect on it resulting in the praying mantis monster to wipe them all out. After that, Kamacuras head straight to the World Trade Center where it proceed to demolish the two towers by ramming and crushing them with its pincers as a demonstration of its power.
Next, we get footage of news depicting monsters all over the world attacking human civilization with Megalon thrashing Africa, Dagahra poisoning Australia, Griffons swarming over Egypt and Anguirus smashing China. This is followed by the appearance of the alien races, the Bilusaludo and the Exif who aid humanity by forming the Earth Union.
In the near future, Akira and Haruka Sakaki are scientists serving under the Gotengo ran by Captain Junguji. They are followed by other scientists including Dr Martin along with bodyguards such as Daichi. The Sakakis are searching under the request of Dr Yamane who discovered a strange anomaly. Having suffered massive casualties by Kaiju, the Earth Union had the Gotengo to find the source and send the data back so that countermeasures can be prepared if it was another Kaiju. Instead there wasn't but a small army of Giant Rats. After a short battle, Deputy Captain Mori arrives along with a squad of soldiers to save the group and the two groups head back to the Gotengo. Just as the Rats were about to overwhelm them, they stopped and fled but one of them was caught under the jaws of Zilla. The Gotengo escape while Zilla pursued the ship with great ferocity that is until it stopped its pursuit and left. Akira deduced that it stopped because they entered a place it didn't like. The Gotengo then discovered they the source of the anomaly Yamane mentioned and found a carcass of Kamoebas.
Arriving at the EU headquarters, the Sakaki reported their findings and concluded with Dr Yamane that whatever Kaiju killed Kamoebas has unlimited power. After the conference, the Sakakis returned to their quarters to see their son Haruo who is still a baby at the time. The Sakakis have dinner and are joined by Dr Martin and Daichi. They are discussing about the recent events including the news about the possibility of space travel. We get to see what the Sakakis were like and we see that the couple are only interested in making a future for their son without the Kaiju.
Meanwhile, a military unit patrolled the area in what was the last base stationed in America. A squad was led by Belu-be who uncovered a battle between Anguirus, Varan and Baragon. This is a battle where the monsters show their different abilities; Varan has gliding and sonic roar attacks, Baragon breaths fire and can dig and Anguirus curls into a ball and also dig. The three halted as they sensed the tremor. That is where Godzilla appears and he shows to these three Kaiju why he is tough. He fires his Atomic Breath many times and crushes the monsters under his heel. Eventually, he kills Varan by slicing him with his spines and then incinerates Baragon by firing his Atomic Breath into its mouth much like FemMUTO. Anguirus escaped by burrowing into the ground. During the battle, a piece of Godzilla's skin came off and is found by Belu-be.
Belu-be reported this finding to the Earth Union who revealed that Godzilla had been a figure of interest. There had been rumors of Godzilla throughout the Kaiju War but no one has seen this Kaiju until now. This news reached to the Gotengo and Akira and Haruka had to go back to work. Before that, they do meet Metphies. There would be a exchange of beliefs before they left with Metphies showing interest in Haruo.
The Gotengo arrives at France where Godzilla was sighted, battling Megalon. However, Godzilla spotted the Gotengo and blasted it causing the Gotengo to crash. Many of the crew survived but some didn't including Captain Junguji. The outcome of the battle between Godzilla and Megalon is left unknown but the survivors managed to reach to a base to be evacuated.
Because of the events that transpired, the Bilusaludo decided to propose an idea; one that will turn the tide against the Kaiju; a machine based on the most powerful lifeform on this planet and that is Godzilla. Time will shift two years later where everyone continues the battle against the Kaiju but it doesn't look good. Most of the world is under the control of the Kaiju and worst of all, Godzilla is heading to Mount Fuji where the most heavily fortified base is there, ran by the Bilusaludo and where Mecha Godzilla is stored. Thus, Operation Great Wall commenced.
Akira and Haruka left Haruo under the care of Daichi while they head to battle alongside the Earth Union against Godzilla. Earth Union tried their best to lure Godzilla away from Mecha Godzilla and into their trap. As they did this, the other Kaiju intervened in their progress. Many Kaiju appeared including Gorosaurus, Rodan, Kamacuras and the Giant Rats causing challenges for the Earth Union. Eventually, Operation Great Wall did succeed. The Earth Union exploded a huge hole into the ground and Godzilla fell into and trapped. The Earth Union cheered that they succeeded and that humanity will thrive. Suddenly, the Gotengo picked up something and it's powerful. The site where Godzilla was trapped started to get red hot. The earth crumbled until it exploded showing everyone a pillar of light. Emerging from what was believed to be Earth's Greatest Victory was Earth's Greatest Enemy, Godzilla. Godzilla once more marched and head to the Mecha Godzilla facility. Belu-Be evacuated his people just in time before Godzilla destroyed the facility.
However, the destruction of Mecha Godzilla wasn't the worst. After defeating Earth Union once more, Godzilla reared his head and roared to the Heavens. A minute of silence later, the earth trembled. What remained of the forces of Earth Union watched in horror as a flock of Rodan approached Godzilla. Later, herds of Kaiju like Kumonga and Anguirus burrowed from the ground. And exiting the forest were Orga, Megalon and Gorosaurus. It was there humanity realized in horror that Godzilla was uniting the Kaiju under one banner, a goal to DESTROY ALL HUMANS! Because Godzilla delivered a decisive blow against the enemy of Kaiju, he became the King of the Monsters.
In the last twenty minutes, Earth Union made a last stand at the facility where the Aratrum and Oratrio are about to launch. The Kaiju army arrived and an intense battle occurred with the Kaiju slaughtering everyone in their path. Then, the scene happened. Daichi took a young Haruo to the ships and they both see the transports carrying Akira and Haruka. However, Godzilla got through the defense line and destroyed a Landing Ship that crashed presumably destroying the transports and presumably killing Haruo's parents. The Aratrum and Oratrio left the Earth.
Back on the surface, it is later learned that Akira and Haruka are alive along with several survivors. They watched Godzilla standing triumphant and roared alongside his army. Humanity has lost and Earth became the Planet of the Monsters. In a credit scene, an older Haruo was researching on the sample of Godzilla and vowed revenge on the Kaiju.