Desktop Defender is a tower defense game featuring towers and monsters (aka "creeps"). The point of the game is to use your towers to build paths and defenses to stop the creeps in their tracks (which come either one, two, or in a special case, all around starting points). If a creep reaches any of the end(s) (usually equal to the number of starting points), you lose a life. You start out with 20 lives and 130 money to buy towers with. If you survive all the waves (10, 20, 30, 50, or 100), you win. You get the score from each creep killed equal to the amount of money it gives you unless you are using the special Supercharge booster, which in that case you get double the points. If you kill all the creeps in a wave early, you get a time bonus. Every life counts as 25 points. That means that if you survive all the waves without losing a life, you get 500 points from that. There are different score multipliers (x1 through x5) that will multiply your score at the end of each wave.

Different maps are included in Desktop Defender as well as some special modes. Every week, there is a new map called the "weekly challenge". The point is to get the gold medal (a specific amount of points earned) as soon as possible.