Thunder Deck is located on one of the decks of the Final Fortress, a huge flying fortress created by Dr. Eggman. Specifically, this track has the players riding on the gun deck of the Final Fortress, which is an outer deck set during cloudy weather. In the background, one can see artillery cannons that rotate and shoot at an undetermined target.
A couple of Eggpawns can be found along this track, which can be destroyed with Wisp power-ups or Power-Type characters. If anyone else besides a Power-Type character collides with an Eggpawn, they will take damage and spin out temporarily. Along this track are also pillars of yellow lasers. If a playable character makes contact with them, they will take damage and spin out temporarily.
The race starts out in front of the entrance to a tunnel that turns to the right all the time. While passing through this tunnel, it the player has to be careful of the laser pillars that move across the road. After leaving the tunnel, avoid the Eggpawns along the road and then turn left. After then making a turn to the right, the player enters the fortress. From there, the racers have three routes to choose from. Firstly, the player can choose either the left or right road that will lead around the energy reactor in front of the road, which produces a laser beam inside it every now and then, for then to remerge with each other again on the other side of the energt reactor. Lastly, the player can take the middle "road" will which will lead straight through the energy reactor. If the player arrives at the wide spring in front of the energy reactor in due time, they will be able to bounce off the trampoline in the middle of the energy reactor, thereby allowing them to take a shortcut. If they time their jump incorrectly however, the player will be hit by the energy reactor's laser and fall into the abyss.
After getting past the energy reactor, the player will pass through a loop, before hitting a ramp that will send them into the air. While flying through the air, the player will pass through a large energy transformer. After landing on the next piece road, the player then follow the road to the right and pass through a loop. After getting through the loop, a fork in the road appears. The road on the left runs around on the upper levels and has barriers on both sides of the road. The road on the right on the other hand runs around on the bottom levels and has no barriers on the sides of it, which makes it easier to drive off-road. In addition, halfway along the road to the right, a gap appears in said road, which the player can jump over. While both of these roads lead to the same road, the one at the bottom is faster. After that, the player eventually leaves the fortress. The player will then have to go through the last series of turns, which have Eggpawns along them. After this section, the player will arrive at the finish line.
Thunder Deck also has its own mirror image version of it where the left and right sides are interchanged.