The Desolate Hope mixes several gameplay styles. On the station and in the simulations, the game is a platformer. You will shoot enemies, collect powerups and bits (money) and upgrade yourself and your virtual battlers. When you enter a mini-simulation (the old arcade style screens) then the game becomes an 8-bit overhead dungeon crawler. There you can farm money and gain options to customize your battle experiences. When you encounter a virus boss, the game shifts to a JRPG style battle where you must use the mouse to select from your various options to defeat your opponent. Almost everything outside of these battles is aimed at upgrading your abilities and increasing your stats for these fights, they are the real challenge of the game.

On a distant edge of an unknown planet, an abandoned structure sits in silence. Constructed by an unmanned research vessel sent from Earth, the Lun Infinus station was designed to run simulations for a five year period, exploring possibilities of human colonization in the case that Earth became uninhabitable. Developed during an age of ambition and wealth, the project was quickly abandoned when interest faded in the following years.

The last transmission from Earth occurred more than thirty years ago. The Lun Infinus station contained five sentient computers, Derelicts, built with certain levels of mobility in the case of emergency or need for relocation. Each of these Derelicts was to formulate their own plan for colonization based on thousands of hours of simulations. Given the amount of time that has passed however, the simulations have become very elaborate and bizarre. Meanwhile however, a mysterious computer virus has emerged. The virus of unknown origins has been slowly ravaging the Derelicts. Because of this, more and more CPU processing power has been needed for anti-virus measures, leaving less power for the simulations. Coffee is the last mobile resident of the station, a small service robot who spends his days keeping the station and the Derelicts operational as they perform their daily tasks. Since CPU power is slim, Coffee has been cutting corners to find ways around the virus. By using small subsystems and less vital CPU's scattered through the station in lesser devices, Coffee has designed a line of digital helpers, each simply called a D-Co, or "Digital Counterpart", to assist him in fighting the virus and keeping the station operational. Eventually the virus gets the best of each D-Co, and Coffee tries to create an improved D-Co using a different CPU. The latest is D-Co 9, built using the code of a simple computer game. Coffee dedicates his own CPU to be used for the main simulations, putting D-Co in charge of moving his body throughout the station, taking care of the needs of the Derelicts, and fighting off virus attacks when they occur.