In SNW: “Those Old Scientists”, the following facts are established:
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Horonium is an element that powers the time portal on Krulmuth-B
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Horonium was once used in the hulls of NX-class starships, officially because it was durable, lightweight and was just the right shade of gray
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The portal on Krulmuth-B had Nausicaan writing which said, “This is a time portal”
The name horonium, as I pointed out in my annotations, comes from the Greek hōra - the root word for horology, the art of constructing watches or clocks. This cannot be a mere coincidence. We can reasonably surmise, therefore, that whoever coined the name for it was aware of its uses in relation to temporal technology.
So the following questions raise themselves:
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Why was horonium used in the hulls of NX-class starships and not anywhere else? What made the NX-class special in that regard?
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Did the Nausicaans really build the portal on Krulmuth-B thousands of years ago?
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Why does the Nausicaan writing simply say, “This is a time portal”?
So here’s what I think: the Nausicaans didn’t build the time portal thousands of years ago. That being said, they did discover it at that time and figured out its nature - that’s why there’s a label on it saying “This is a time portal”.
If the Nausicaans had really built it, then why bother labelling it like that and with nothing else? It’s not as if they were leaving instructions, or wanting to share with other species. As we’ve seen, most Nausicaans don’t rise above the level of thuggery and as a species they seem just a step up from Pakleds in the bright bulb department. And for a species like that, a simple label is par for the course, comparable to the Pakleds naming their capital city Big Strong City.
I think that the Nausicaans of thousands of years past used the portal to jump ahead, perhaps to try and raid futuristic technology to advance their civilization. But in doing so, they attracted the attention of the powers fighting the Temporal Wars. Because of that, the discovery of an ore that could power time portals came to light.
Horonium may not just be a fuel source - its use in the hulls of NX-class vessels shows that it was part of the ship’s outer structure as well as being used in components like whatever that gas-cylinder like thing was that Spock pulled out of the floor of the Enterprise. Why use a metal that has temporal properties? Could it be that it was used as some kind of protective armor against temporal attacks, against enemies that could change the timeline?
The NX-01 was using polarized hull plating before shields were commonplace, so it’s not a stretch to say that horonium could be used as temporal shielding like Voyager in VOY: “Year of Hell”. And the horonium shielding was used in the NX-classes - on the hull and on key components - because that was the first era when Earth got caught up in the Temporal Wars.
So why did horonium run out? There are a few possibilities. One is that there wasn’t that much to begin with and all were used up in the NX-classes or other Federation ships that fought in the Temporal Wars. Another is that the Nausicaans just frittered away whatever horonium was left on Krulmuth-B in their temporal raids and just stopped because they ran out. Or it could be that the wars targeted sources of horonium so participants couldn’t use its shielding properties. Or it could be a combination of all these things.
So to tl;dr: why doesn’t horonium exist anymore? Because the Nausicaans used it, the temporal powers noticed it and then it was either all used up in ship construction or destroyed as a strategic resource.
Damn it, Nausicaans!
For one, the Temporal Cold War was supposed to be over by that point, and time travel would not become a common thing until Spock discovers time warp. We know there was a brief conflict with the Romulans at some point around this time. However, the interesting development in that war was supposed to be cloaking devices, not temporal weapons. Besides, Starfleet should have been upgrading to proper shields by then, not retrofitting hull plating. And I'm pretty sure the shade of grey comment was a joke. We know that even by the TNG era, they don't pay much attention to color-matching hull plates.
What does it mean for a Temporal Cold War to be “over” when cause and effect don’t necessarily come in sequence, anyway?
The shade of gray comment was a joke to us, but Boimler was, as always, in deadly earnest. Anyway, I’m just putting this out there - if you don’t buy it, it’s okay, but I think it’s a decent stab at explaining what might be going on.
Ok, so here's an alternate theory: Horonium is actually tritanium (or maybe duranium) that has been saturated with temporal radiation. As for why they mentioned the NX class being built with it, perhaps the Enterprise's temporal adventures were classified. Starfleet told everyone that all the ships were made with honorarium to cover up the truth.
That might work, but it adds a detail that in my opinion isn’t really necessary and it doesn’t explain why people think you can’t have any more horonium when a scan might reveal its true composition. It’s simpler to say horonium is what it is with its unique properties.
It also complicates things by having Spock’s attempt to create horonium being needlessly hazardous if all they needed to do was infuse some metal with chronitons (and in any case Spock’s experiment was basicaly transmutation, so he must have felt that there was a way to create horonium through nuclear processes).
Well obviously it didnt work and Spock was not optimistic about his odds. Also, Spock is the guy who evenually cracks the riddle of time travel, so he may have been working off some early half formed theories of temporal physics.