Godzilla 3 Possible Storyline

The story for the third and final film is based on Mothra, Rodan and King Ghidorah all appearing in the second film where all three die except for Godzilla. The movie would be a crossover of Godzilla and Pacific Rim, however none of the characters from Pacific Rim are in this film.

Featured Monsters/Jaegars:

Godzilla

Gamera

Bagan (Completely different design and traits though)

Gypsey Danger

3 Other Jaegars 

Featured Characters (Just made up the names really quickly)

Dr. Serizawa

Tom - researching on Bagan

Megumi - researching on Gamera

John - researching on Gamera

Aki - girl who bonds with Gamera

Saito - Aki's father

Ben - Main character for Gypsey Danger 

Steven - Ben's partner for Gypsey Danger

The movie starts off with some background stating that due to the fact that there have been so many monster attacks in the past couple of years. world countries have worked together to create Jaegars to combat future MUTOs so that people can stop completely relying on nuking big populated cities to solve the issue. The Jaegars are based in Hong Kong.

A massive meteor hits Japan in the area near Mt. Fuji. When people discover it's impact site, the meteor created a massive hole in the earth. It's also discovered that there are very high amounts of radiation in the site. Among the researchers of this project, there is Dr. Serizawa, and an American, Tom. They later find a series of tunnels down near the bottom of the impact site, but are unable to explore them due to high radiation levels.

Deep sea researchers, including John and Megumi, about 100 miles north of the Phillipines discover a very unnatural sea floor, and do some further invesigation. They discover that the floor has a massive bump in the shape of an oval. Researchers place some experimental devices on it, which awakens it, causing it to move, and release tons of amulets from it's shell. Throughout the rest of the movie, the researchers observe the object, which is moving towards Japan slowly. 

I haven't thought much about what happens in Hong Kong with Ben and Steven but some human sub-plot could form from that, before they're needed later in the movie. 

A late teenage girl, Aki and her father, Saito are spending the day at the beach. Aki is collecting shells and discovers an amulet. She thinks that it's very interesting and decides to keep it. Later in the film, the amulet turns orange, signaling that Aki has been bonded with Gamera. 

Godzilla then shows up at Osaka, and seems to be heading north towards Tokyo. Gypsey Danger along with 3 other Jeagers are sent from Hong Kong to Japan. Dr. Serizawa believes that it is the radiation emmitted from the impact site that has lured Godzilla to Japan. 

Megumi and John return to Japan to their research factility in Tokyo, while other researchers keep watch on the moving object at sea. Saito sees a news broadcast on television about the giant object and immediately recognizes one of the amulets that is shown. He then speculates that it might be what is the cause for his daughters recently strange behavior. 

Dr. Serizawa and Tom follow the radiation tunnels via helicopter with a detector and realize that the tunnels are heading in the direction of Tokyo. 

Saito brings his daughter to the research facility where Megumi and John are at, and tells them how his daughter has changed as soon as she found the amulet. When Megumi and John try to figure out what the cause for it is, the ground starts to shake temendously and a giant monster comes out of the ground in Tokyo, Bagan. 

Night falls on Tokyo and a strong thunderstorm comes into the city. Saito, Aki, Megumi, and John all go to the nearest refuge facility from the research facility. 

Godzilla soon appears, and begins to fight with Bagan. About 3 minutes into the fight, Gypsey Danger and the 3 other Jeagers arrive. Gypsey Danger takes on Godzilla while the other 3 take on Bagan. 

The researchers observing the giant moving object notice that the object is rising and gaining speed. The object starts whirling around in a circle very fast and blasts out of the ocean, heading for Tokyo. Gamera arrives in Tokyo and immediately begins fighting Bagan. When the commanders of the other 3 Jeagars realize that Gamera has no business  with them, they help him fight Bagan.

While this fighting is going on, Aki runs out of the refuge facility due to her extreme bond with Gamera, and Saito, Megumi and John all run after her. She manages to get to a rooftop in order to see the ongoing battle with Gamera. The others catch up, and decide to stay because they fear that leaving the area would be too dangerous. Tom and Dr. Serizawa spot them all on the rooftop from their helicopter, and land. Just when they both get out, the helicopter is crushed by a falling building. 

Bagan seems to be pretty powerful, and takes on 4 enemies at once very easily. Over time, 1 then 2 then all 3 of the Jeagers are destroyed by him. Gypsey danger puts some resistance towards Godzilla but Godzilla eventually overpowers it, and blows his atomic breath into Gypsey Danger's nuclear reactor core, destroying it. When Gyspey Danger falls to the ground, Steven has a broken leg, and Ben helps him get out of the Jeager though it's eye. 

Dr. Serizawa, Tom, Saito, Aki, Megumi and John all leave the rooftop because the battle was getting closer to them. On the streets, a building comes down, killing Megumi, and splitting up the group, with Dr. Serizawa, Tom and John in one group, and Saito and Aki in the other. 

Bagan blasts off a part of Gamera's shell, causing Aki's amulet to break, and she falls unconcious. Saito brings her to a nearby military medical center in a park. Dr. Serizawa, Tom, and John are all rescued by helicopter later on. 

Gamera finally ends up killing Bagan by absorbing fire from nearby explosions, and punching his fist into Bagan's heart region, and blowing a fireball right at it. He is then attacked in the back from an atomic breath.

During the fight between Godzilla and Gamera, Godzilla ends up biting off one of Gamera's tusks, Gamera manages to pull apart one of Godzilla's arms, and Gamera also is able to blow off half of Godzilla's face. Gamera then finally uses his mana attack on Godzilla resulting in a huge explosion. Believing he has killed Godzilla, Gamera turns around and starts heading to sea. Suddenly, a red spiral ray comes from behind, and shoots right through Gamera's shell and torso, stabbing him. Godzilla had absorbed the incredible mana energy that Gamera had blasted him with, and the result was burning Godzilla. 

A mortally wounded, and dying Gamera tries to escape, but burning Godzilla gets up close to him, and blows off Gamera's head with his Spiral ray. 

Right after this, the Prime Minister of Japan was just notified that thousands of other meteors sharing very similar features to the one that landed in Mt. Fuji, have landed all around the world. He is also told that there are many Bagans wrecking havak around the globe. 

The final scene is burning Godzilla heading out of Tokyo, and preparing to fight about 20 Bagan monsters seen in the distance.

Well that's it! I hope you guys liked what I think would fit as a grande finale, so please let me know what you think!