In the distant future, humanity has entered a golden age and has colonized Mars. One day, contact was lost suddenly from an asteroid mining station. This was found to be caused by an invading hostile extraterrestrial force known as F.A. (First Approach ). To defend against the aggressors, the Solar System Defense Forces developed and deployed the R.A.I.N (Remote Artificial Intelligence Network), a remote guidance system for the Antares-xx, an unmanned combat vehicle.
Border Down features difficulty settings that are switched during gameplay. There are three difficulties to a level, called "borders", green being the easiest whereas red is the hardest. The green "border" is the longest variation on a level, but the enemies fire far less frequently. The red "border" is the shortest variation on a level, but the enemies fire at a frantic rate, making it increasingly more difficult to stay alive.
Instead of receiving a set number of lives, a player has the option to start on any "border" at the beginning of the game. Whenever the player dies, a "border down" occurs and the game continues onward on the next hardest difficulty. This puts increasing pressure on the player to stay on the green (easiest) border. Conversely, a player can opt to start at the red "border" for the maximum challenge. The game ends if the player dies while on the red border.