It's clear that monster attacks are a regular thing for SpaceChem. The "accident" at the SpaceChem station mentioned in the first story page is very heavily implied to be a monster attack that Angela lived through. In "No Need for Introductions," Bruce doesn't react to the monster with surprise, but with decisiveness; the kind of decisiveness he'd only have if he's seen this plenty of times and has learned how to react.
This kind of thing would be impossible to keep under wraps; it doesn't matter what kind of non-disclosure agreement SpaceChem made its employees sign, sooner or later someone would say something, or someone would take pictures or make a video. How did SpaceChem keep it secret for so long, then?
The answer is in how Bruce shows up to talk to the protagonist after each boss mission. After "Exploding Head Syndrome," the protagonist says "my thoughts evaporated" as Bruce is talking to him. Bruce talks to all the survivors of each attack. The words he says are about the importance of SpaceChem's mission, but what he's actually doing is subtly using his mind control to make his employees want to keep the monsters a secret.
The monsters can do things that are unknown to science. The unidentified elements are unknown to science. Coincidence? I think not.
This would also explain the WMG about Bruce having mind control powers. Bruce understands the elements enough to make a laser and missile out of them that can counter the abilities of the monsters; it wouldn't be a stretch to say he's found a way to use them to enhance himself. (Maybe some sort of pharmaceutical chemical he takes?)
- The omega element is used for destruction, which is why it's an ingredient in laser dye and the missiles for the Prometheus.
- The sigma element might be related to controls, or conditionals. In "Freedom of Choice," it's used to make the laser react to the different colors of the monster; this is a conditional. In "End of the Line," it's used to hold the Phantom Battleship in place and disable its phasing ability; this is the part that relates to control.
- Not sure what the other elements do, since we never see their products in use.
The monsters need time to possess someone. Joel wasn't taken over right away, but instead had that period of time in which he was having headaches. Near the end, Bruce is described as looking unwell, tired, and desperate. He must have recognized the symptoms and was trying to finish Prometheus before the end.
