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:
Anyone Can Die: And will. If there is a named character, they are probably doomed, usually due to one of the local horrors you're unfortunate enough to encounter on your journey. Notable deaths include Joel (blanked and put out of his misery via gunshot) and Tim (exploding head).
Artistic License - Chemistry: Although the game is reasonably accurate with regards to certain details, and is in fact used as educational software in chemistry classes for certain topics, most of the chemistry is vastly oversimplified, inaccurate or plain impossible. Most notably, near the end of the game, the reactions introduce elements that don't exist.
Earth-Shattering Kaboom: Fail to defend your control center, and the proprietary Reaction Mediation Device in said center annihilates the planet—which includes you. At least in theory—the events on-screen are a simulation, and a failed solution means only means you go back to the drawing board.
Eldritch Abomination: The last level on each planet (save the tutorial) is a battle to destroy one of these. They typically end up remotely possessing and/or causing the gruesome deaths of several named characters, and killing large swathes of the company's local workforce in their rampages.
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 labelled with Greek letters. Also, the fictional elements.
Hoist by His Own Petard: Implied in the Alkonost boss-battle. Said boss is introduced as a "Defiler-Alchemist". In that level, you sort "tainted water" pumped from the sea; apparently some of the hydrogen atoms in the water have been transmuted into uranium. (Artistic License - Chemistry at work here, since those molecules would be unstable IRL, and would look nothing like water.) You then feed those same uranium atoms into a particle accelerator to fire the beam that kills the boss.
Leaning on the Fourth Wall: Certain levels are named "Prelude to a Migraine" and "No Ordinary Headache". It makes complete sense with the associated story chapters, but as you would expect, this is where the game starts throwing curveballs at you (randomized input, etc.).
Level Editor: The Journal of Reaction Engineering, which contains a comprehensive editor and nearly 200 official user-made levels.
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, the titular company. They primarily deal in exploiting exoplanets for resources, but dabble in most anything else that is necessary for them to be self-sustaining during lengthy space missions.
Nintendo Hard: The game is infamous for its rapidly increasing difficulty level. Only a handful of players have ever had the patience to finish the game, as by the end, designing a solution can take a dozen hours or more, depending on if the basic concept is sound or not.
Remixed Level: World 6 level "Danger Zone" and World 7 level "The Blue Danube" are identical, the only difference being that the latter is where you are introduced to the flip-flop command.
Shout-Out: One level is named "KOHCTPYKTOP", after a previous work (Kohctpyktop: Engineer of the People) by the author. The level has you produce silicon fragments, which are the main element you use in that game.
Speed Run: The game includes statistics on how fast other people's reactions ran, how many reactors they used (in production levels), 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".
Stealth Pun: One of the user-made puzzles requires you to sort a randomized sequence of hydrogen and helium atoms, without access to a sensor. The name of the level? "Nonsense!"
Another user-made puzzle requires you to correct impossible isomers of sodium hydroxide; the name of the level is "Lies" (a pun on "Lyes").
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.
Unobtainium: With fusion reactors, it's possible to make atoms of elements of very high atomic number (up to 109), some of which in reality are postulated to exist but cannot be sustained for any realistic length of time.
Elements Θ, Ω, Σ, and Δ.
A cross-promotion with Team Fortress 2 added a new set of levels based on the Australium atom.
Unperson: You — it's heavily implied that sometime during or after the events of the ending, SpaceChem expunged every last trace of evidence of your employment.