Nintendo of America had requested that any blood or nudity couldn't be shown in the Super Nintendo version, otherwise they wouldn't release it. Blood was either suppressed or changed to green, and the crack of the naked alien's rears was reduced by 3 pixels.

Interplay wanted to replace all the music in the Genesis and SNES versions with new original tracks. Eric Chahi, the game's designer, requested to at least keep the original intro music to help retain the atmosphere but Interplay wouldn't agree. To express his frustration, Chahi sent them an endless fax with the message "keep the original intro music" in big letters with the ends of the paper taped together to form a loop. Interplay did reconsider however when Delphine posed legal action.

In the 3DO version, entering the code BRGR (a reference to Rebecca "Burger" Heinmann, who ported the game to 3DO) will access a hidden game called stalactites, in which the goal is to destroy stalactites before they get bigger by getting under them while dodging balls, somewhat like the opposite to Breakout.

After the release of Future Wars, Eric Chahi had a choice to help fellow programmer, Paul Cuisset, with his next game, Operation Stealth, or make his own game.
Chahi was confident enough in his programming and the tools available at the time to begin his own project.

Developer, Eric Chahi, was impressed by the flat-color animations that the Amiga version of Dragon's Lair had, and thought that it would be possible to use vector outlines to create a similar effect using much less computer storage.
After testing the graphics on several platforms, he found the Amiga had the most optimal framerate.

Though Eric Chahi had tried to use smaller polygons (which he called "pixigons") to construct the backgrounds for the scenes based on Deluxe Paint artwork, the process of creating them was infeasible, which resorted in him using bitmap images.

Eric Chahi planned on creating a science fiction game that was similar to Karateka and Impossible Mission. Because he wanted to create a dramatic, cinematic experience, the game featured no HUD or dialog, only giving the player information about the game world through gameplay and cutscenes.
However, with no idea of the technical limitations he would face while building out the story, he focused more on creating ambiance, rhythmic pacing, and narrative tension in the game.