I keep thanking u Pistachio. You didn't have to do it if you didn't want to. I wasn't gonna strangle you anyways
(For now)
Dunno if i went by your edit's lines too much. Im kinda reluctant to abandon the blue-green-orange ramp.
But went back to darker colors, added some variety to the walls and retouched stuff here and there. I also think the readability problems are a little compesanted now. Opinions?
As for the story, I might be influenciated by Vortex 2, a game so similar to Portal 2 that many people believes it's the same game (hint: it is).
Jokes aside, this is the kind of story one invents while drawing.
And even though TripleM's dobuts have been vanished, i'll answer:
I use Super Awesome Automatic Pixel Art Creator! which if you take the "automatic" word out leaves you with Photoshop.
It also created this: