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We've found a habitable planet orbiting a red dwarf star some light years away and conditions are Earth-like enough that a colonization project was initiated. Before any humans landed on the planet, a thorough, extensive reconnaissance of the planet was done.

After we reached close to the planet, we parked the colony ship in orbit to get housekeeping done. We surveyed the surface from orbit, we did tests on the weather, we sent out probes nearby and studied the star carefully. Probes and drones were also sent through the atmosphere to figure out its makeup, and then to the surface. We brought back samples of microorganisms and the local flora back to study and see if everything is kosher from a safety standpoint.

The only caveat is that we did find ruins of some kind of advanced civilization on the planet, but no signs of the actual inhabitants themselves. The study of the planet is not cursory - we've been examining it for years with our colonists waiting in cryosleep. No stone is going to be left unturned.

But here's the thing - there actually are intelligent aliens on this planet, and for their own nefarious purposes, they've been hiding from humans until they're ready to show themselves.

So my question is - how did they manage this disappearing act, with us combing the planet with a fine-tooth comb for signs of life. To make it easier, let's say that the population for the aliens is fairly low for a Earth-sized planet. Let's say there are about 50,000 of them on the planet.

What could they do in order to stay hidden? Underground habitats perhaps? Maybe we didn't think to look too deep below the soil and they managed to stay unnoticed?

What are some other ways they could hide?

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    $\begingroup$ Cute critters turning out to be intelligent... For example the tree-cats of Sphinx in the Honorverse. (They are telepathic, so it took them quite some time to realize that humans were not dumb animals and communicated through the noises they made.) $\endgroup$
    – AlexP
    Apr 9, 2020 at 22:55
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    $\begingroup$ @Faz The "space-travel" tag is inappropriate for this question; "space-travel" is concerned with getting from point A to point B (often via the bypass at point C), not with what happens once you get there. Perhaps would the "colonization" tag be more appropriate? $\endgroup$ Apr 9, 2020 at 23:01
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    $\begingroup$ Small furry humanoids that don't use fire, and their language is in the supersonic range. Little Fuzzy by H. Beam Piper. Or the aliens are dangerous apex predators that don't use fire or tools. Novice by James H. Schmitz. $\endgroup$
    – NomadMaker
    Apr 10, 2020 at 10:01
  • $\begingroup$ @AlexP, exactly the example that came to my mind. It helps that treecats were below the size thought to be necessary for intelligence, and their population was such that they don't have big, obvious cities. Also, because they aren't at the top of the food chain, they tend to stay hidden, and it helped that they could see and avoid most traps, including wildlife cameras. Humans had settled Sphinx before anyone even saw a treecat. $\endgroup$
    – Matthew
    Apr 10, 2020 at 15:29
  • $\begingroup$ @Faz, if you haven't read it already, you really should read some of the earlier treecat stories ("A Beautiful Friendship" and "The Stray" in particular). The situation you're describing is almost exactly what happened with humans and treecats (sans the ruins and nefariousness; treecats just had a healthy caution for "two-legs", helped, no doubt, by the fact that we (humans) showed up in flying conveyances and with great big honking guns that could easily kill giant predators. $\endgroup$
    – Matthew
    Apr 10, 2020 at 15:32

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I can think of quite a few ways this can happen. The main variable is to do with the survey performed, so I'm going to talk about that, as this will determine what you want to go for.

So, firstly, planets are very, very big. What you've described as a survey could easily miss even an intelligent race that's not trying to hide. So, you sample the atmosphere, you send probes to certain locations and you have stuff up in orbit. But, did your colonists image the planet?

If the answer is no, then maybe they just sent down landers to certain areas and there was just no life there. Maybe there were only so many landing sites they could be bothered to do. If the aliens are concentrated then you might just miss them (this also works for primitive intelligent aliens, they could be surprisingly hard to to find if they haven't spread to the whole planet yet).

It gets harder for technological life, since the main way we would detect them is by emissions in the atmosphere, or radio leakage. But if there's a small number, their emissions might be undetectable and unremarkable. If they are careful and don't leak radio emissions (say everything is cabled, for security), then they'd be fine. If they had no reason for lighting, they could even live on the surface and you'd never know. I could imagine a technical hive society living that way and there are probably others.

But, let's assume your colonists have actually imaged the planetary surface and taken high resolution pictures. We can do this already to 1m resolution. So any structure would be seen.

But the next question is, what does seen mean? Well, if humans pour all their attention on each individual image, that would be a lot of work. It's more likely they'd get some AI to look through them all and detect "Civilised Structures". But if the alien's definitions are very different to humans, then the AI won't flag them up. Even humans looking at them manually might not know.

Assuming a good optical survey is completed and anything alienish would be detected, what next? Well, maybe the survey focused on habitable areas and not all the planet. But habitable to whom? If the aliens are different and think, say, polar regions are really nice and good for life, but humans are more "let's be near the equator, because the planet is cold and the equator gets close to nice" then we'd just write off an entire area as "not worth survey". It might get cut for funding reasons.

OK, the colonists are anal and have surveyed everything How could the aliens hide?

Well, in one Anne McCaffrey story, humans accidentally colonise a planet belonging to aliens because the aliens came, set things up and, because they had teleporters, went back home for the winter, because winter's cold, man.

On the other hand, maybe the aliens hibernate. Maybe they just went to sleep because the planet has some really harsh variability and it makes sense. Say it gets irradiated every year for a month, and everything that can goes underground or shuts down and is adapted to it (note, you said Red Dwarf, and this actually happens with solar flares, but you may also have to worry about tidal locking with those for your planet). Intelligent life would be in underground shelters having a snooze, or maybe they'd live underground so as not to bother coming up to the surface all the time, or going down. Maybe humans came during a spell when everything looks normal, but life hasn't resumed yet. Maybe the original survery was during a downperiod due to coincidence. Maybe the aliens have woken up and gone "OMG there's an alien spaceship orbiting us, let's not go topside just yet!" and have the structure to hold out a bit because they're adapted to do that for one or two periods in an alien year.

In the tidal locking scenario (where the planet stops rotating because it's close to the Red Dwarf) maybe the aliens live on the night-side, where it's permanently night, for reasons. Maybe they evolved that way.

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    $\begingroup$ "did your colonists image the planet?" Not imaging the planet, especially when you're already in orbit, would be incredibly stupid for a whole lot of reasons. I think it's safe to assume that they did 😉. " I could imagine a technical hive society..." One wonders if we'd recognize Formics as intelligent? What if they're sessile? $\endgroup$
    – Matthew
    Apr 10, 2020 at 15:37
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    $\begingroup$ I would point out that we are still discovering things on earth now, such as the occasional new species. That is only possible on the basis of centuries of exploration. Even with advanced tech, any new planet will be much, much less explored than earth currently is. $\endgroup$ Apr 10, 2020 at 18:39
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I have to give partial credit to gianluca, whose answer inspired this, but... what if

They live in the ocean

If your aliens live underwater, and especially if they only live in deep water and don't hang around shores, they will be very, very hard to find unless you go looking for them. In particular, an orbital survey is very unlikely to spot them, and humans probably don't put a high priority on exploring the ocean depths (after all, we aren't going to live there...).

Granted, they will have trouble with "civilization" (metalworking is next to impossible) unless they also have underground industry, but just maybe their technology is advanced enough that ocean-dwelling is possible and preferred for whatever reason; this could explain the ruins on land.

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    $\begingroup$ "Something's alive in the ocean!" $\endgroup$
    – Muuski
    Apr 10, 2020 at 21:50
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    $\begingroup$ Love this one, and an ocean-dwelling species is something I was leaning towards. It actually works out really well because I've been wanting to have a cosmic horror angle to the story. So having deep-sea cthulhu-like creatures that were awakened because of humans meddling around would fit in really well with the story. $\endgroup$
    – Faz
    Apr 11, 2020 at 15:48
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    $\begingroup$ @Faz They could be incredibly light sensitive for some parts of their suns natural spectrum, so they live in areas that don't ever get any sunlight. That might have evolved after they already established an advanced civilization, e.g. through a pandemic which corrupted their genes, so they already had the technology to build deep sea habitats. Most of them didn't fit into the new habitats, so of their billions of inhabitants only a few thousand survived. They only move to the surface wearing cthulu-like protective battle suits. $\endgroup$
    – user48721
    Apr 12, 2020 at 10:20
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    $\begingroup$ Perhaps we could combine this with @aphenine 's answer; the sun has been particularly aggressive with its solar flares in recent years, and the ocean just so happens to be one of the thickest, densest natural radiation barriers on the planet, which is why they relocated from land to the ocean. $\endgroup$
    – Brinstar77
    Mar 31, 2022 at 13:09
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The intelligence is an emergent property.

Your colonists did find the aliens, and even took some back to the ship. The aliens have a life cycle that involves several morphs. Currently they are microscopic and amoeboid, distributed about the planet, living as micro-organisms do.

Like a slime mold, at a certain cue these micro-organisms assemble and agglomerate. They differentiate, taking on different roles in the new, multicellular organism. These new organisms are things that the colonists have not seen. They are interesting and dangerous.

You could have this happen several times. Each iteration in the life cycle is different, more complex and larger. The final stage are the intelligent beings, possessed with racial memory and great intelligence. But sustained intelligence is dangerous over the long term for a species, and the intelligent ones last only a certain period before once again reproductively dispersing as microbes.

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    $\begingroup$ While this is fascinating, what mechanism would cause them to all 'revert' to the non-intelligent phase at the same time? $\endgroup$
    – Matthew
    Apr 10, 2020 at 15:38
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    $\begingroup$ @Matthew if know there are mayflies on earth and you go looking for mayflies right now, why don't you find any? They are all in larval form at the bottom of rivers is why. In may when the adults emerge you will find plenty. Then none in August. It is not at all outlandish that lifecycles could be synchronized species wide. Different things use different cues to synchronize - season, moon phase, or longer and more mysterious periods like the cicadas. $\endgroup$
    – Willk
    Apr 10, 2020 at 16:28
  • $\begingroup$ Hmm... maybe. I wonder what effect it would have on a civilization if everyone is "asleep" for all but a few months out of every year. I suspect agriculture and animal husbandry would be difficult to impossible, for one... $\endgroup$
    – Matthew
    Apr 10, 2020 at 17:55
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    $\begingroup$ @Matthew depends on what kind of agriculture. You could certainly set up a situation that encourages the growth of certain kinds of plant life and discourages others. Domesticating animals does get tricky, though, if the animals are not on a similar cycle. $\endgroup$
    – Ben Barden
    Apr 10, 2020 at 18:49
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    $\begingroup$ @Matthew - beyond the scope of the question but imagine the intelligent final phase. They awaken knowing all that their ancestors knew. They set about getting their planet in shape to host the generations of non intelligent young that their planet will host: eradicating predators, remediating ecology etc. They are like visiting angels. I could imagine it might be difficult for the intelligent ones to build spacecraft in their short time. Commandeering a space ship to colonize a different world would fall in their wheelhouse. $\endgroup$
    – Willk
    Apr 10, 2020 at 19:10
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The entire alien population is a military outpost

50,000 is a very small population for an intelligent species. This suggests that this is not an entire civilization, but an occupation force. The ruins indicate that there was an alien civilization here once, but this second civilization that they are at war with came along and wiped them out, leaving only a small garrison to protect their newly acquired planet.

The key difference between this being a civilian colony and a military outpost is that military has a vested interest in operational secrecy. This means that this base will be obfuscated by the best concealment technologies these aliens have at their disposal be it cloaking technology, holograms, Faraday cages, radio absorbing materials, etc. The humans did not find them because they are using hiding technology specced out to be able to hide from people far better at finding things than just human colonists.

When the humans arrived in orbit, their military doctrine did not give them any reason to attack the humans since they were not at war with us. But, once humans landed on the planet, it was seen as an invasion so they defended the planet as they were supposed to. Not only does this explain why they were hiding to begin with, but also gives a very valid reason for them to come out of hiding to attack even though the planet is clearly big enough for both peoples to co-exist.

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It depends on various factors. To begin, 50.000 people on a earth-like planet are really few (in fact about the double of the village where I currently live). So here some options.

If they are scattered on the planet, also in small groups, you basically miss them since the footprint of a single alien, or a small group of them, can be really hard to find (or really likely to overlook) and a single/small group of aliens can hide really fast and easily. Think a cave

If they are all in one/a couple of village, it is still easy to miss them if not performing a full planet image scan and also in this case can be missed. You know how a human village and its inhabitants looks like, but alien can be completely different in shape, both for construction shape and dimensions. So you simply overlook them, which is way more probable if your scouts don't perform the full planet scan. The footprint of a village (or some of them, but smaller) can be relatively big, but this depends on the technological level: if they are at a industrial age, you can have some spot with some peculiar emission which can expose them, if you can identify it as such. On the other hand if they are an agricultural society, the footprint is way smaller and then again, what you think is a cultivated field can be totally different from what the alien considered a cultivated field, so you simply see a forest and not the aliens that cultivated it below.

You are looking in the wrong places, maybe the aliens live in some habitat you does not consider habitable (extreme cold or heat, deep caves, deep underwater, some other exotic habitat).

Since the scouts found some ruins, the aliens are the survivors of some advanced civilization that had to face some catastrophic event that decimated the population or they are settlers themselves and they survived hiding in a deep cave under the sea, isolated from the outside. Add some advanced technology like the replicator from Star Trek and a clean and abundant energy source and they can live for quite some times in the cave. I know that this generate a lot of other problems, but I suppose they are smart enough to solve them.

You are looking for a living being but you have no idea how it can be, so you don't recognize it. After all, how the alien looks like ? It looks like a human ? Like a rock ? A giant snail ? An octopus ? How can be sure that this strange object is not a living being with a life cycle of some centuries ?

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How intelligent are the aliens? It could be possible that they live underground in a particularly harsh area of the planet. Like The Australia or The Badlands of your planet. And have developed a cloaking device of some kind. I doubt humans would bother searching too much in a place like that so the device wouldn't have to be too high tech. Maybe a disrupter or disrupting plates like on a stealth plane to make the ground penetrating radar read their compound as a solid object or not there at all? Are the aliens completely humanoid? Could they not live deep in the oceans? Or perhaps have an Atlantis type structure on the ocean floor with the same radar disrupting technology

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  • $\begingroup$ Also, if they are particularly advanced, perhaps they hid on an uninhabitable planet nearby waiting for them to "take the bait" $\endgroup$
    – Jane Doe
    Apr 9, 2020 at 21:31
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The ruins don't belong to the intelligent species that is living on the planet now. Since the ruins look like they could be useful for the human colonists, the survey teams are looking for a roughly humanoid species living on the planet. The current inhabitants are definitely not humanoid, and don't live near the ruins since they are not configured for their needs. These aliens are also recent arrivals and their colony is small and partially hidden as a defensive precaution. Since their structures are not laid out for a humanoid species and are in places not generally used by humanoids(steep cliffs, glaciers), they are mistaken for large social insects or something similar.

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  • $\begingroup$ Yeah, maybe like animals or something like that, or anything that's not human. $\endgroup$
    – Leviathan
    Mar 6, 2021 at 1:12
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Their Technology is Biologically Based

All of their structures are grown rather than constructed and are intentionally made to blend in to their surrounding ecology. Likewise, they have no need of high density power sources, crop farming or broadcast communication let alone high concentrations of metals or mining.

Food and medicine are all easily harvested from locally available organisms. Made articles are easily constructed by hand from biological sources. Communication and transport needs are handled via grown optical fiber, flying or walking organisms.

The ruins are what is left of a previous civilization that managed to kill off almost all its members. The survivors are those who managed the transition to the biologically based economy. That can also provide a basis for hostility to newcomers.

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You saw what you wanted to see

What the bots recorded and what there is are two seperate things. The light/radiation from the red star has a weird effect on everyone, but the aliens are unaffected and specifically choose that planet for that reason, which makes you collectively into an hypnotizes-like state which makes you see what you want to see.

Then by the time you get to the planets and realise it's not as pretty as you thought, it's too late: You're stuck in their metaphorical web and they can now do the nefarious things they do.

You could make a small story about one specific panicky person who wasn't hypnotized, getting confused why everybody says the planet is nice when the stats clearly say it's not, trying to warn everyone but getting written of as weirdo.

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Giant intelligent antlike colonies. They were surveyed and dismissed, as the samples only returned individual ants. Had your colonists looked closer, they would have seen that although each ant is pretty small and primitive, they have high bandwidth communication due to complex pheromones. The production of pheromones was not noticed during the survey, as the captured samples didn't emit any in captivity. However, taken as a whole, the entire colony is capable of very intelligent reasoning. It also keeps its intelligent activities below ground. This lets you develop intelligent aliens which are without technology, yet can conduct complex strategies, be difficult to exterminate, and which can pull surprises from underground if threatened.

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Space Junk

This idea is partially taken from Skyward by Brandon Sanderson, where a thick layer of space junk acts almost like a shield for humans defending their planet. In your case, the aliens saw the humans coming, and then vacated the planet's surface into the junk that's stuck in its orbit. They wouldn't quite be on the planet, but they could zip down whenever they need to using whatever transportation they have to gather resources or do whatever they want on the planet's surface.

They're part of the planet

It could be that what the humans mistook for geological formations were actually incredibly large, very well camouflaged aliens that don't move that much. Maybe they communicate telepathically, or through other geological means such as tectonic plate motion. Weird concept, but I kind of like it.

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You avoid people looking for life by being in a place where life is not expected. Or no life relevant to the colonists, to be more exact. The survey will cover the entire planet superficially but only areas that look attractive to colonization or likely to support significant native life will get the full treatment. The colony will take care of the rest organically as it grows and develops. No need to waste survey resources on it.

The first choice to think about is the why. Why are they hiding when the surveyors arrive?

They could have had advance warning. Maybe some smuggler or pirate already made contact with the natives and they have a very good idea of what to hide from and when and a very bad idea of what the humans are like.

It might be religious. Maybe they are not so much hiding as avoiding spoiling the sacred home world. They would have abandoned their cities and withdraw into to remote and hostile areas. And built everything to leave as little mark as possible. Including being totally invisible from orbit.

Or they might have needed to hide to survive and never had reason to stop. This would typically be the result of an apocalypse scenario. Usually a great war with weapons of mass destruction lobbed at anything that makes itself noticeable. Maybe an actual doomsday weapon was used. If the surface is covered with lethal viruses or berserk killer robots, you will stay low and you probably won't be in a hurry to stop doing so. Maybe you are the second aliens to come calling and first visitors make humans seem nice.

The second choice is the actual place. The where of the matter.

The deep sea would be a good choice if the aliens can survive there. It is very large and remote enough that the initial survey would not look at it very hard. They'd basically just do some spot checks to see if it is similar enough to Earth to be unlikely to be dangerous. A civilization trying to stay hidden would easily be overlooked.

The surviving would be fairly hard. Your aliens would probably need to be capable of surviving without air for it to be practical. Simplest solution would be genetic engineering. This would dodge the issues with developing technology under water or having cities full of pictures of underwater cities.

You would be not only fairly hard to find but also rich. There are lots of minerals and geothermal or nuclear would give enough power to grow as much algae as you want. IF you keep the system fairly self contained, so that your colonies do not leak excess oxygen, it should work out.

Your aliens might also just be the afore mentioned killer robots. Robots do not need to breathe and can be constructed to handle almost any environment. A civilization of robots and AIs would also have few of the signs people would look for when looking for life or people.

Underground can be practical, if you are underground in a remote and inhospitable area. In practice this means a desert. It can be a hot desert like Sahara but Antarctica would have suitable spots as well. I'd still recommend a hot desert since it makes hiding the heat signature easier but a survey might not bother to check if that underground heat in the polar continent really is from volcanism. Not like the colonists will want to live there anyway.

They might also be off-planet. Maybe they survived on the moon or the asteroid belt. And dig deep underground to avoid radiation. Your planetary survey might totally miss this because it looks at the habitable planet. This would work better with the advance warning option.

And last there is the simple option of camouflage. If your aliens look just like a rock or a tree or a hive of insects or something else that exists in large numbers, the survey would have a good chance of sampling only the harmless version. Camouflage good enough to trick survey drones is unlikely to evolve naturally but robots designed for warfare or genetically engineered species would be able to do it. Survey droids are not intended to deal with military hardware or deliberate obfuscation.

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How alien are they. So much so that they don't appear to be "life", but rather "lyfe". Maybe they didn't build structures but the structures are in fact dead aliens, or more interesting, a game that they do for mating or entertainment. Maybe the aliens are having their own internal strief and the structures are the result of feud or symbolic attempt to make peace. What ever the structures are, humans think that people should be inside them and the aliens think something completely different. In fact, maybe the humans build their own huts, out of the remenants of the structures, so of course later, it turns out that they have been using the aliens to fabricate the walls or the roofs or carpets, etc... and then a hut catches on fire and its shear chaos as the humans inadvertently trigger a mating ritual (because a dead alien is really just an alien not looking for a mate) of flying fiery carpets enveloping anything they can find including a few colonists..... drama ensues... practically writes itself. Insert "rug burn" joke here. Colonists swear vengeance. Aliens swear undying affection. Burning cyclically continues. Humans develop PTSD. Aliens need to check into their own version of rehab. Nobody wins.

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