A significant part of Bowser’s army in the Super Mario games is made up of Koopa Troopas and the flying Koopa Paratroopas. As I’m sure you all know, they’re turtles. Well, tortoises, technically, since they live on land. Have there ever been turtle enemies on the aquatic stages of a Mario game? Anyway, they first showed up in Mario Bros., which called them Shellcreepers.
If we go by the old idea that this game took place before Mario and Luigi came to the Mushroom Kingdom, or perhaps while they were temporarily out of it, this could perhaps be seen as the early stages of an attempted Koopa invasion of New York. There were several episodes of the Mario cartoons where King Koopa tried this. Anyway, the first Super Mario Bros. established the Troopas as hiding in their shells when jumped on, and their shells then became weapons, albeit ones that could hurt Mario and Luigi as well.
In fact, I think the SMB instruction booklet was the first place I came across the word “ricochet.” The game also introduced the winged Paratroopas, whose wings would fall off when they were stomped.
I’m not really sure whether turtles with wings evolved naturally or were the result of experiments by Koopa scientists and wizards. Mushroom World genetics remains a largely unexplored field. The “para” in “paratrooper” refers to parachutes, which the turtles don’t seem to have. Flying enemies in later games also tend to have “para” in their names, even though it doesn’t make a whole lot of sense. The Troopas and Paratroopas are color-coded, with the green ones just walking in a straight line, while the red ones patrol back and forth along a surface. I seem to recall seeing mentions of the red ones being stupid, presumably because they don’t go anywhere, but they also don’t walk into pits like the green ones do. But is it something in their genetic makeup that makes shell color match up with behavior, or is it more of a rank thing? Maybe if you’re promoted from guard duty to actually advancing on the enemy, you get a shell color change. Super Mario World introduced two new shell colors, and also the ability of the plumber heroes to knock them out of their shells. This was a very cartoonish concept, perhaps heightened by the fact that this was the first game to show Koopas walking on their hind legs and wearing shoes.
In real life, a turtle’s shell is part of its skeleton.
The Paper Mario games bring in friendly examples of many species normally found working for Bowser. The Koopas (not called Troopas since they aren’t part of the military) live in villages like the one found in Mushroom Kingdom in the original Paper Mario, and are willing to help the plumber against Bowser. A winged Koopa named Parakarry works for the post office, and serves as one of Mario’s allies.
Whether they’re former subjects of Bowser’s who defected or there have always been some Koopas who weren’t under his rule isn’t specified. The Thousand-Year Door identifies a Koopa (along with a Toad, a Goomba, and a Boo) as one of the heroes who defeated the Shadow Queen 1000 years previously, but we have no idea what Mushroom World politics were like back then.