The Koopa Troop is nearly unstoppable. Bowser has an almost unlimited supply of Goomba and Koopa and Shy Guys. Despite having a huge military, the Koopa Troop is continuously defeated by the Mario Bros.
The main force of the Koopa Troop differs from game to game. Koopa Troopas are quite obviously the most intelligent of their widely-used members and Magikoopas, Hammer Bros. and Koopatrols are among their elites. Also, strangely, Yoshi's Universal Gravitation seems to suggest that Fly Guys, who were constantly seen commonly during Bowser's cutscene-illustrated operations, were the Koopa Troop's main soldiers. The Yoshi series seems to suggest that back while Bowser was a baby, the troop's main force mainly consisted of Shy Guys.
The Koopa Kingdom is where Bowser is at the time.
1: Supreme Leader
Baby Bowser (in the past)