Unlike Tiger General's fortress, Bowser's fortress is more futuristic. It is divided into six main sections.
The first section, at the bottom, is the fortress's main entrance. As seen from that section, the Koopa Kingdom in HTFA 6 is also futuristic-looking and far more developed than Happy Tree Kingdom. Rivers and pools of lava can be seen as well, fitting more Bowser's typical territory. Once one enters the building from said entrance, one can see a tall chamber filled with platforms to stand on. One has to climb up those platforms to proceed further. In the next room of this section, lava can be seen being dumped from pipes. Flame emissions are also commonly seen, often bursting from the flowing lava. After climbing up another vertical chamber, the next path can be seen, which leads to Mecha Dragon's room, located in the dome part.
Further through said dome part is the fortress's second section, where electric traps are commonly found. It is said to be the fortress's generator room because of those hazards. Like in Tiger General's fortress, this section also contains seemingly-toxic water that is safe to swim in. One vertical chamber in this section contains Force Beam traps that have to be avoided quickly as they deal the most damage in comparison to all other hazards and enemies. Mecha Neena is the boss of this section.
The tall blue tower at the eastmost part of the fortress is the third section, considered to be the heating room due to its intense heat and lots of fiery hazards. Mecha Tacho guards this section.
The central hub of the fortress, located above the dome section, is this fortress's fourth section. This leads to Bowser's lair, but Bowser has prepared a flipped-out Flippy to deal with trespassers. After that, the fifth section consists of a large elevator that leads to the top of this fortress where Bowser's mech is placed and the climactic battle against said mech and Bowser himself takes place.
- Apparently, Bowser's Fortress is similar to Mr. X's Castle from Mega Man 6, although it has a Bowser emblem instead of a letter "X".