The Star Trek Universe is a Simulation

I like your hypothesis, and I like your writing. However, I think your hypothesis works even if the Q are not AI, but instead agents of the "real universe" ("Agent Smiths")

How do you square this with the Q apparently being quite mortal after all?

I started thinking about the nature of the Q the other day when rewatching the Voyager episode “The Q and the Grey”; it seems odd that an omnipotent/omnipresent species would also be so rigid and unimaginative. Why, for instance, do the Q have such strict rules about suicide? You can argue that they fear their species eventually being gone because they all eventually opt to off themselves out of boredom with existence, but as long as they had the ability to die that is unavoidably going to be the eventual outcome of an organism that can exist for infinity (mind-boggling, isn’t it?) anyway.

Probably because it was something that had never been done or happened before, and it's something that, at least for them, is an irreversible process. As far as the Qontinuum is concerned, Quinn deciding to die could start punching holes in the universe, or spell doom for them as other Q followed suit (being able to fill the gap didn't seem possible, or wasn't an option they were willing to entertain). They weren't entirely wrong, since his death kick-started a civil war.

Then you have the fact that the Q are not just invisible observers of the universe; they interact with species and even individuals to, seemingly, drive outcomes that are possibly part of a preferred order to things. Quinn influenced Earth’s history to drive certain changes; helping Newton define gravity was certainly a big event in human scientific growth. Why, though? What is driving the Q to pursue certain outcomes in evolutionary history?

From what we see, it seems to be less aiming for specific outcomes, and more generalised tomfoolery. Just as Q might muck around and cause trouble, other Q like Quinn might want to try and help various species instead. Although I imagine that they are both subject to the same rules as other Q, of "don't make a mess". As Q points out, the Qontinuum is a boring place to be.

It's also worth pointing out that there isn't really a generalised, singular goal to it either. Quinn might have helped some individuals over the course of history, but he hasn't specifically directed the growth and evolution of humanity. The only being we've seen do that is Q, who may or may not be under direct orders from the Qontinuum.

And why is it such a disruptive event in the Q Continuum for two Q to have an offspring? Obviously a species that can live forever doesn’t need to procreate, but it’s clearly possible so why is it so shocking?

They don't really see themselves as similar to limited, mortal beings, so the idea that they could have children as Q, without having to don a mortal body, and go through all that business, was unprecedented. Q Jr was the first (and possibly only) Q child.

It had never been tried before, and that it was a success was quite shocking, as it also meant that Q who did opt to die could do so without causing the Qontinuum to be permanently diminished. It's worth noting that even Q didn't try it with another Q without Voyager's prompting. He went to the Voyager and tried to solicit Captain Janeway instead, so it might have been thought to be an impossibility.

Now step away from the Q and look at the characteristics of the Star Trek universe. The Milky Way galaxy alone is chock full of humanoid alien species that (for the most part and with variations/outliers) breath the same air, can live within a certain range of temperatures, have brains/emotions/standards that function similarly enough that ideas and principles can be shared and abided by, and interbreeding is even possible to a certain degree without outside support. That’s huge. And though the show tried to explain this a little bit in “The Chase”, I think it’s fair to say that we’ve seen humanoid species across the galaxy to a degree that a shared ancestor isn’t enough to explain it all.

It doesn't really have to. The progenitors in that episode aren't the only progenitors around. There are a few other species that almost certainly meddled, and spread things around more of their own accord, as well.

The Arretans are implied to have seeded life on Vulcan, for example, and they're a different alien species altogether.

Couple that with some genomes being spread around through some means or other, then it's not implausible that there would be some level of mutual compatibility, extended even further by the development of warp drive, and everyone working on technologies to make them all compatible with each other, like the Barzan and Benzite breathing devices, which supply them with poisonous gases that they need, but also protects other humanoids from exposure to those gasses.

Beyond biology, let’s also look at the makeup of the physical universe: subspace allows interstellar communities to function without succumbing to the laws of relativity: FTL travel is possible; real-time or at least near real-time interstellar communications function; the materials needed to facilitate warp drive are ubiquitous enough that nearly any warp-capable species that wants to travel into space can get it. It is arguably miraculous that the universe in Star Trek can operate the way that it can, and these things do not conform to our current understanding of how the universe and space/time operate.

However, that is also generally put down to us having an incomplete understanding of the nature of the universe, and how it works currently.

Much like the hypersonic series in the periodic table, where dilithium sits, which doesn't exist to our knowledge, subspace is just another part of the universal laws, previously undiscovered. They have their own version of the same issue, where conscious thought is another aspect of the universe, which does not confirm to either our, nor the Federation's model of the universe.

Taking all of this together, I propose that the Star Trek universe is a complex simulation, designed purposefully to simulate what the universe would be like if it operated by certain principles that would allow for interstellar communities to form and that many humanoid species existed and were capable of interacting with each other. Several instances of this simulation are running simultaneous with similar parameters but modified to generate different outcomes: the Mirror Universe, for instance, has different presets to create more aggressive humanoids less likely to work together. Furthermore, I submit that the Q are AI programs designed to interact with and shepherd these communities into developing in such a way that they would eventually develop the right levels of technology and understanding to grow into a spacefaring species.

This is a naturally unprovable premise (similar to the "It's all a dream" theories), but if that is the case, wouldn't allowing cross-simulation communicability contaminate the simulation?

We already know that one of the reasons why the Terran empire came into prominence is because of future technology that they accidentally obtained from the Prime universe, which means that any growth simulated and observed would no longer be natural, or accurate to the starting premise.

I'm also not sure about the Q being AI, or being arbiters of spaceflight in that case. It's fairly clear that the Q do not see themselves as protectors or guardians, or else Q's mucking around with various species would have been met with more stringent restrictions (if the idea came to him in the first place).

We also know from "Encounter at Farpoint" that the Q wished to do the opposite with humanity, considering them to be "too savage" for space exploration, threatening to send them back to the stone age or thereabouts, which would be both too late if they wished to shepherd humanity into spaceflight (they had at least 200 years of spacefaring history at that point), and counter to their "mission".

I know this isn’t a provable hypothesis and it’s really just an idea for fun, but it kind of (in my opinion) adds another dimension (no pun intended) to a species like the Q.

The idea is definitely fun, but I also think that it might make sense for something other than the Q. Bringing it back to the Q seems to make it all run into "small universe syndrome", if all seemingly-omnipotent entities are Q, just as all aliens are related to humans in some shape or form.