Quantum Particle State Analyzer 6000 is a hovering machine about 40 ft. above ground, between Mineral Processor 3000 and Autobuy 2000. It acts as the save point for the game, preserving your Upgrades, items, cash, and hull/fuel states, but immediately resetting your score. It is recommended to save every time you return to the surface to keep your progress in case you have a game over or the game crashes.
Saving does not save your personally dug tunnels, and everything underground will be reset upon game over or crash.
Right after beating the Ending, you will be given a chance to save the game, the only time you can do so without visiting Quantum Particle State Analyzer 6000. Whether you save or not, you don't get another chance, and will be sent to the starting screen of the game and your save (or lack thereof) will take effect.