First, the good: The scenario you've picked has a lot of potential for visual charm. I can imagine the underground environment, containing some human artifact being illuminated by small shafts of light, & some primitive subterranean creatures warily puzzling over it. & it's neat. I'd play it.

But the backstory might be a bit unwieldy. The more elaborate a backstory is, the more it tends to burden the narrative. It forces you to violate the storytelling principle of "show, don't tell".

The pacing is important - How are you going to tell the audience about these past events? You'll need to parcel out the events in the backstory in an intriguing way, & make sure you don't resort to dull exposition sequences, ie. wizened old sages blathering on, or an intro text crawl. Even the most thoughtful background information won't be compelling if it brings the current narrative to a halt too frequently.

Streamline the exposition & omit unnecessary details - for instance, if the fact that there happened to be 4 original robots never emerges as a significant plot point in the current narrative, then omit it - it's a red herring. Eyecraft addressed this with the innocent-human element.

Finally - this might be at odds with what you're trying to accomplish, but do you have to have a backstory at all? Really: what if the story began with the Monster Dilemma, on through the Robo Solution, & then progressed to the Sub-Terrain Mystery - now you've got a three-act structure!
Just a thought.

Also: the robots' role seems to take a sudden shift in the plot outline - they aid humanity by destroying the monster (good thing), & the first one you find runs away from you (cue sympathy), & then suddenly you have to destroy them! I know they're hollowing out the Earth & all, but by that point I'd already been primed to like them!

End.

Hi there.

I think I see some of those "jaggies"[...]

You can fix that at the lineart stage a bit.

 For instance, try to have the lines transition smoothly from 1px per row to 2px per row. If that makes sense.

& an additional source of jaggies is the AA on the outer-edges, which would look nice on a black space background but looks spotty on the forum colors (generally when you have AA on the outer-edges, avoid transparent BG (or use alpha))

When I first saw the finished image I briefly thought the fin was the wing on the opposite side (viewed from slight above angle), which was crazy. I think I saw it that way because the shading on the wings is similar to the fin, so they look like they could be oriented in the same direction. Quick edit might help...

[...]is there is some proper rule or orden in between the shades, or if we just must use which colour looks enough darker/bright and nice for the viewer in a gradient of pixels.

Well, you can get an idea of how many intermediate shades are necessary by looking at old games with less color depth.

These are the amount of shades of gray available to 24bit, 15bit (SNES), & 9bit (Mega Drive), just to illustrate. & the Mega Drive had some beautiful games like this.
But ultimately, you just eyeball it.

[...]using 1x1 brush for art, they use 2x2 brushes to make the pixels bigger and use the 1x1 ones for smaller details.

Well, there are at least two different approaches to the the beginning "construction" stage. A) Draw an outline or wire-frame model (line-art, typically 1px), or B) Draw large blobs of shade & sculpt them into the appropriate shape (>1px). I favor approach A because it's the way I'm best at visualizing 3d objects, & it feels neater; others like B. Experiment.

Nice job! Only a few crits, really. Here's a quick edit!

It's almost perfectly clear to me. Just the area between the neck & shoulder is ambiguous. I don't think there's a contrast problem - characters can contain multiple elements with distinct colors.
I would:

• fix-up neck/shoulder area
• remove the shading on the thought bubble - let that be purely symbolic.