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Divers - Just a group of scientists studying sea life and exploring the oceans to understand it to advance knowledge. Armed with spear guns, but only to protect themselves as a last resort as their mission is to study sea life.
Aqua Raiders - Like the divers they are explorers of the deep but are more hostile to sea life instead of co-existing they actively defend themselves against it in order to acquire treasures. Armed with spear guns to defend themselves as they recover treasures. Clearly some have died in the process from sea life, a few sets have skeletons with divers helmets on from previous expeditions, their lost comrades. Perhaps this is why they are so well armed. The sea life is pretty hostile.
Hydronauts - A group of supposedly good guys fighting the Stingrays, but their real goal is securing resources in the oceans. Are they really "good guys" however? Much like the other factions they are exploiting the sea crystals disrupting the sea life while fighting off the Stingrays, but is there more to this story? Why are the mutant Stingrays so tirelessly fighting the Hydronauts? Perhaps there is some history between these factions, the Hydronauts hardly have the expression of friendly undersea explorers... They are evil for this reason.
Aquanauts and Aquasharks - Supposedly a "good guy" faction, they really don't seem to be doing much good. They disrupt the sea bed with their large base and disturb the ecosystem by mining for crystals in the ocean, god knows the kind of pollution created by their machines for excavating and digging out crystals. They're not much better than their foes the Aqua Sharks who seem to have a similar goal to exploit the oceans, perhaps Aquanauts had a more noble goal with their resource extraction while the Aquasharks pursued something more sinister, without knowledge of what the crystals were used for however this is hard to discern motivations, so Aquanauts are lawful neutral, Aquazone neutral evil.