[4] Having defeated the Grand Intellect in Invasion of the Vorticons and saved the Earth, eight-year-old child genius Billy Blaze is still forced by his parents to eat his vegetables at dinner.

Giant helmet-wearing potato men tell him that their king Boobus Tuber has brought him to their land with his Dream Machine, and Keen is now his slave.

Upon defeating Boobus Tuber and turning off the Dream Machine, Keen wakes up in bed at home, where his mother informs him it is national "I Hate Broccoli" day.

In October–December 1990, a team of employees from programming studio Softdisk, calling themselves Ideas from the Deep, developed the three-part video game Commander Keen in Invasion of the Vorticons.

The group, who worked at Softdisk in Shreveport, Louisiana developing games for the Gamer's Edge video game subscription service and disk magazine, was composed of programmers John Romero and John Carmack, designer Tom Hall, artist Adrian Carmack, and manager Jay Wilbur.

After the release of the game in December, and the arrival of the first US$10,500 royalty check from shareware publisher Apogee Software, the team planned to quit Softdisk and start their own company.

Keen's red sneakers and Green Bay Packers football helmet were items Hall wore as a child, dead enemies left behind corpses due to his belief that child players should be taught that death had permanent consequences, and enemies were based loosely on his reading of Sigmund Freud's psychological theories, such as that of the id.

[6] For Keen Dreams, the team reprised their roles, and used the game as a prototype for what they wanted to change for the next Keen games for Apogee: an increase in graphical quality with parallax scrolling to make the background move at a different speed than the foreground, a pseudo-3D view rather than a side-on view, ramps rather than solely flat surfaces, support for sound cards, and changes to the design based on player feedback.

[1] For Vorticons, Carmack had created adaptive tile refresh to produce a scrolling effect on computers not powerful enough to redraw the entire screen when the player moved.

[5] He also removed the pogo stick from the game, both to symbolize that Keen was in a nightmare and therefore felt less empowered, and also to make designing the levels easier as vertical motion did not need to be as accounted for.

[2][5] The level maps were designed by Tom Hall and John Romero, using a custom-made program called Tile Editor v5.0 (TED5), which they used for the entire Keen series as well as several other games.

[9] Bobby Prince had planned out an introductory cinematic with an accompanying song titled "Eat Your Vegetables", but it was rejected as it would have made the game too large to fit on a single floppy disk.

[2] The story introduction was instead done in plain text, and "Eat Your Vegetables" was repurposed as stage music for Commander Keen in Goodbye, Galaxy.

[13][14] In June 2013, developer Super Fighter Team licensed the game from Flat Rock Software, the then-owners of Softdisk, and released a version for Android devices.