Seeing as *this* project is also almost done, I'd like to give it some basic Lore to retrofit it back into the games universe:
The game takes place in one of parabolic void dimensions that has has physical matter transported into it. The thing you're drilling into isn't infinite, it's just absurdly large (this should be indicated in-game and maybe even tie into the Transmitter location). Deep depths should wrap back around to the top and vice-versa presumably once you're able to warp.
You're an automaton "employed" by the Zenith universe's version of Tangle, who has a different name (S.E.R.A.P.H.) and more of a solid purpose (protecting against the Labyr threat) so doesn't have genocidal tendencies. This could then also tie into the Automaton and other space- themed games Lore wise, wrapping this whole new slew of games together in one neat bundle.
The thing you're drilling into is a massive Labyr artifact, a kind of "waystation" between the Zenith universe and Labyr Honeycombs. There's a Transmitter somewhere that draws upon the massive amount of power generated here through metal/crystal/rock gradients to coordinate cross-dimensional transport. Like with Omega, destroying this would deal the Labyr a pretty deadly blow.
This universe is unfortunately very hostile to Automatons-- the physics don't work right, so whatever limited thing gets through is going to have to use the native materials to reconstruct itself.
Parabolic cyclical causality is *weird* -- past attempts at bringing Automatons in instead led to native metal deposits that the Labyr found and were able to use to construct their machine. Your whole goal here isn't shutting the transmitter off, but pushing its energy back in the machine to return it to pre-Labyr conditions -- Tangle knows this is possible because it's already happened and will happen an infinite number of times -- the timing is set up to have this be in play around the time the rest of the war is happening for maximum benefit before the Labyr regain it again.
Basically every time Tangle transported a fleet of Automatons into the space they instead warped into native metal pockets, seeded by the Driller. then when the Labyr tried to transport in an Ark, it shattered from the metal, the Labyr were then able to use the combination here to build their waypoint machine. So the actual Transmitter *is* the Driller, which is a far-future version of you, and what you're actually doing is merging with it and then collapsing the Machine to return it to the starting conditions.
Given this, the way Tangle was able to send in a Driller that actually kinda works is because the other one fed him information on one of the Automaton fleet attempts. You shifted into the native materials but it was done in such a way that your knowledge and mechanics were intact and you're able to use the other bits of automaton to get yourself up to full capacity again.
Every time you upgrade you get a bit of Lore. Presumably this has to do with the information about the world / your purpose being encoded in the upgrade blueprints. So the order you unlock things probably matters and you have to unlock everything to get a full idea -- but then also you have to unlock everything to get to the endgame anyway.
The amount of game seeds corresponds with the amount of actual Waystations -- in canon it's assumed they were all successful and all turned off at the same time. The games are basically identical in every other respect.
