This was a really nice comment to read, thanks for posting it! This game didn't end up getting a ton of engagement, so its super fun to hear that someone played and enjoyed it this much.
I've thought about posting the story on its own somewhere, but to be honest I don't really know where I would. If you'd like to extract the story to read later, you can copy and paste it from the source code (right click the canvas and select 'inspect' The whole story is inside TextFiles.js, or you can just enter kTextFiles on the js console. It will take some formatting, but feel free to copy/paste it to a doc if you'd like to read it again later. I did work with a game publisher for a chunk of 2019 to create a sequel, but unfortunately had a spat of bad health and had to drop the project. Maybe it'll come someday in the future :)
To answer your question, the other colors are meant to represent the pressures Rich applied to the colonies he tested in order to pressure them into mutating - bacteria, other fungal colonies, or the immune systems of his test subjects.