Throughout the maps, we see the same inventions the humans used to defeat the flying saucers now being used to project barriers on the maps. Not only are they trying avoid the same situation which lead to the creation of the giant monsters but also limiting the damages the monsters create to a small enclosed area all the while sending in the military armed forces to deal with them.
Congar's backstory reveals that he was once a chimpanzee who the species in real life are proven to be more aggressive than gorillas.
Preytor eating the scientist is a reference to female Praying Mantises eating their male counterparts.
Kineticlops being a giant eye covered electricity is one big pun to the saying, "Eye of the Storm".
In Adventure mode, why did Mecha-Congar confronted solely the Player monster rather than prioritizing both them and Preytor? Because the military programmed him to do so as they deemed the Player monster as the greater threat after they destroyed both their robots, Robo-47 and Goliath Prime.
Vegon is a giant venus flytrap that birthed at the center of a nuclear plant. In other words, They're a Power Plant.
However it isn't the nuclear energy that created Vegon, it's the alien fuel that did it. As shown in the Atomic Island intro cinematic, Kineticlops had taken over the nuclear plant and contaminated it with the fuel. So when Atomic Island exploded, whatever traces of the alien fuel left created Vegon.
That same fuel was also spewing from the central reactor hence why the monsters' energies are replenished.
The poster for the Tsunopolis level translates as "Destroyer Wave". It's both fitting that not only there are massive tidal waves as the hazards but that said waves were created by Cerebulon whose title is "Destroyer of Worlds".
It's also funny that whenever a monster throws something at Cerebulon's saucer, Cerebulon gets pissed and sends a tidal wave as payback.
The reason Cerebulon did not do anything when the monsters fight in Tsunopolis is because he is waiting for them to tire themselves out and step in to collect who is left.
We also get a hint of this at Club Caldera where the flying saucers take active part during the fight between the Player monster, Agamo and Magmo.
Fridge Horror
Since we saw dozens of ships crashed landing onto Earth, there's no telling how many more giant monsters are created. Even worse that as shown in the cinematic intro, some of the saucer's fuel had came into contact with humans.
In adventure mode, after Togera and Preytor died, it's likely the military have taken their bodies and turn into cyborgs much like what they did to Congar. If their mecha versions that act as alternate skins suggests, they succeeded.
