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In SpaceChem, you are a "reaction engineer" in charge of running chemical processes through literally nanotechnological processes: you pick up atoms from one end of your reactors, add and remove bonds to transform them into the desired atoms or molecules, and then spit them out the other side. As the game progresses, you end up with more complicated inputs -- from single atoms to molecules to randomized assortments of molecules (which then must be sorted and shipped out) and beyond.

As you progress through the game, a plotline is slowly revealed, starting as you begin your employment at the eponymous company, SpaceChem.

This game provides examples of:

  • Art Major Physics: Chemistry doesn't actually work like this -- molecules are three-dimensional, a machine to pick up single atoms could never be built, different elements are different sizes, etc. -- but that doesn't really matter, does it?
    • And to be fair it does have a fair amount of actual chemistry; such as atoms only having so many bonds (except that Nitrogen cannot have 5 bonds. It doesn't have enough empty orbitals for it). It does flub up though with the complicated machines. We already manufacture many of the product chemicals, and the whole process they're using is incredibly over elaborate. Chalk it up to Rule of Fun.
      • Technically nitrogen could have 5 bonds - 4 covalent bonds when positively ionized, plus one ionic bond (the game doesn't distinguish between covalent and ionic bonds), e.g. ammonium chloride. However, ammonium compounds won't fit into the game's square grid...)
  • Boss Subtitles: For the Eldritch Abominations below.
  • Breather Level: The tutorial stages when they introduce new tools.
    • "Danger Zone", a level on Hephaestus IV, is a simple bonding/sensor mission in the middle of a planet filled with rotations.
  • Earthshattering Kaboom: Fail to defend your control center, and the proprietary Reaction Mediation Device in said center annihilates the planet. Which includes you.
  • Eldritch Abomination: The last level on each planet (save the tutorial) is a battle to destroy one of these. Unfortunately, they are played all too straight, remotely possessing and causing the gruesome deaths of several named characters, and killing large swathes of the company's local workforce in their rampages.
  • Elements Do Not Work That Way: See Art Major Physics. Near the end of the game, the reactions introduce elements that don't exist.
  • Future Food Is Artificial: One of the products SpaceChem manufactures is ... fish cakes. Apparently, that's all SpaceChem employees get to eat.
  • Gratuitous Greek: The input and output regions are labeled with Greek letters. Also, the aforementioned fictional elements.
  • MacGyvering: Defense missions always require you to supply a machine built from whatever you have on hand at the base. One memorable boss requires you to turn a transport rocket into a nuke, using water as your only raw material.
  • Mega Corp: SpaceChem.
  • Nintendo Hard: Starting with the planet Alkonost, which features levels like "Prelude to a Migraine" and "No Ordinary Headache", where the game starts throwing multiple molecules down a single input.
  • Speed Run: The game includes statistics on how fast other people's reactions ran, how many reactors they used, and how many symbols they used in their reactors, giving Challenge Gamers at least three realms on which to compete.
    • There are also certain in-game challenges to beat particular times on levels, starting with "Complete 'Nothing Works' in under 1000 cycles".
  • The Blank: Quororque does this to Joel, to the absolute horror of the protagonist.
  • Unexpected Genre Change: While most of the levels have you designing machines to meet quotas of output molecules, the defense missions require you to design a machine that you can use to respond to external events.
  • We Have Reserves: SpaceChem has a lot of "unfortunate accidents" and "anomalies" at its colonies. Doesn't stop them from expanding across the galaxy.
  • Your Head Asplode: Tim's fate.
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