I am writing a science fiction short story, which is loosely about terraforming. The drama takes place on a terraforming site, which has been halted, in its early phases, due to the discovery that the planet goes through an uninhabitable period in its cycle. It could be every 50 years, or it could be every 250 years, the time and duration of the events doesn't really matter, but something must happen to the planet, which would render it uninhabitable for a period. The event has to be something that wouldn't be spotted at first. The people wouldn't start the difficult process of terraforming/inhabiting the planet if they knew they'd have to abandon it. If anyone has any ideas and could get back to me that would be really helpful.
Natural cycles of uninhabitable periods would have been discovered during the surveys and preparation before the terraforming started. Instead of a natural cycle the planet had an apocalyptic war in its past. This war was fought by vast armies of robots and killer drones. The sapient alien population went extinct during the war. Eventually the fighting machines destroyed each other and the war seemed to have ended.
But deep beneath the surface of the planet gigantic automated factories produced the robot armies of both sides in the conflict. Every two hundred years the robot armies re-emerge from underground bunkers to wage the war all over again. Until each side has destroyed the other. Then the war pauses for another two hundred years.
Scavenger robots scour the surface of the planet recovering construction materials of metals, plastics and equipment parts to feed the subterranean factories. Anyone visiting the planet between the war periods will not find any sign of the war. Every wrecked war machine and its parts will have been taken below.
Bacteria can survive being frozen for extremely long periods - potentially as long as 100 Million Years. It's not implausible that a small pocket of bacteria, buried underground or in permafrost, would go undetected during a planetary survey. Bacteria are also suspected of radically changing the earth's atmosphere to the oxygen-rich atmosphere we know today - killing off most of the anaerobic life on the planet in the process. It seems plausible that you could have a similar kind of bacteria that changes the atmosphere in a manner that is hostile to human life - giving off Carbon Dioxide (or Monoxide, perhaps). It could be awakened from dormancy by a change in the planet's temperature; perhaps the end of an ice-age, or even deliberate warming caused by the terraformers. This actually has real-world parallel for today's changing climate: the re-emergence of Anthrax in Siberia.
As a4android said, anything about the solar system that produces periodic challenges to the habitability of the planet should have been noticed during an initial survey, provided the surveyors were competent. And as for the planet's weather systems, water cycles, and so on, those get remade in the course of terraforming.
However, if the survey was incompetent, and missed a problem, then you can have a periodic problem that wasn't spotted. If that degree of incompetence is compatible with your story, a heavy meteor shower might be a useable idea. Read the Wikipedia article about meteor showers, and then come back.
Now, to make this work, you need the meteors to be much bigger than usual, and tightly concentrated in one small region of their orbit around the star. That means that in most years when the planet crosses the orbit of the shower, you get only a normal meteor shower, of tiny meteors. However, when the group of larger chunks of debris happens to be at the crossing point when the planet reaches there, you have a lot of big meteorites and those would disrupt the terraforming process (since we have only general ideas about how to do terraforming, having it be disrupted could be plausible).
What I haven't figured out yet is how to achieve this fairly tight group of bigger chunks of debris. Maybe someone else can suggest that?
My answer would depend upon the orbital situation of the planet being terra-formed.
It's possible your planet could have a lengthy orbital period in a circular orbit. It could also be a fact that your planet is part of a double-star system or a single-star system with a moon-sized object in an eccentric orbit.
Either way, the orbital interactions could be such that your planet experiences close passes to the other bodies such that your planet experiences extreme seismic/volcanic/tidal events everywhere on the surface. Maybe the orbital mechanics are such that this happens for a 5-year span every 10,000 years.
You'd have to develop the complexity of the orbital mechanics of the system.
Another possibility is that your planet could orbit a star that explodes into extremely intense solar flaring every 10,000 years that literally engulfs your planet for periods of weeks or months, enough to dramatically reduce food supplies for decades.
As @a4android pointed out any competent solar survey team prepping a solar system for terraforming should catch anything too terrible before starting, but that's assuming they are competent. Try thinking less of crew of the Enterprise and more of a bunch of over worked, under paid solar surveyors that falsified a few reports, and maybe didn't do all of the due diligence necessary to catch that horrible disaster speeding towards your planet.
Also don't forget the politics. Maybe the civilisation that started the project collapsed into civil war leaving your planet on its own for 50 to 250 years.
In short never underestimate the power of people to mess things up.
What about a tidally locked world? In order for the planet to be properly terraformed it would have to be set in motion again. The process could be slow and laborious and take 50 to 250 years before it could be occupied. Or set in motion with one almighty spin that would leave it uninhabitable for many years because of the terrible tectonic stresses it would cause.
There is another planet in Pern's solar system with an elliptical 250 year orbit. At the far end of its orbit it reaches the system's Oort cloud, pulling material into the inner solar system and into the path of Pern's orbit. The result is that for 50 years of the 250 year cycle Pern gets showered with material from the Oort cloud. The surveyors (and subsequent colonists) were aware of this, but meteor showers aren't particularly worrisome.
However, the material from the Oort cloud doesn't just form harmless meteor showers - it contains what they call thread, "thin silver filaments of a space-borne mycorrhizoid spore that devours all organic matter that it touches". In short, a deadly rain. However it doesn't completely destroy the natural flora and fauna - they've adapted to the situation such that enough survive threadfall and are able to bounce back quickly enough that the survey team coming a few decades into the 200-year gap didn't see anything concerning.
In the books, the settlers stick around because 1) their voyage was intentionally one-way so they have no choice and 2) the planet has miniature, fire-breathing, teleporting dragons that they are able to genetically modify into a rideable size.
So what should you do in your story? First, remember that uninhabitable for people is not the same thing as totally uninhabitable. Your mechanism of uninhabitability can make it impossible for people to survive, even though the local flora and fauna can. This also makes it harder for a survey team to flag the planet as dangerous, as they won't see the evidence of massive die-offs.
Second, you can make the conditions seem innocuous except for when the disaster is actually in progress. In the case of Pern, this is something space-based that is only dangerous once it gets inside the atmosphere.
For example, what about venomous periodical cicadas? These cicadas only emerge every 13 or 17 years (depending on the species), but emerge in massive numbers. What if, instead of being harmless, they had a venom that was particularly deadly to people? In their larval form they live underground, so while they're not swarming you would have no clue they existed.
If we are to assume the system is well surveyed then perhaps we should consider threats from outside the system.
I hypothesise a pulsar in the same area of the galaxy. The direction of the radiation beams emitted by the pulsar is determined by its magnetic field. The magnetic axis is not aligned with the rotational one, hence the pulsing effect. The beams trace out two cones shapes as they rapidly rotate.
This is where some handwavium may come in as I don't know if this is possible for a pulsar. This pulsar has a cycle where its rotational axis changes, as the Earth's does. As the rotational axis changed the traced cone would narrow and widen.
If your system was at one end of the cycle it would be blasted with radiation from a nearby pulsar at the maximum of each axial cycle. Then there might be hundreds of years before another full cycle completed and the death cone returned.
The surveyors would be aware of the pulsar I assume but they may be forgiven for not inspecting the axial cycle of a object many light years away.
Most of the good takes on this idea that I have seen involved biology. In the case of the movie Pitch Black, there is a biological organism that periodically "spawns" and swarms all over the surface of the planet, consuming everything. In the case of the Anne McCaffery Pern series, the planet periodically came very close to a wandering planetoid covered with an extremely hostile alien life form that was able to drop into the upper atmosphere of the colony world, but only every so often, and only when the planets were sharing an orbit (so there were many year gaps where the wandering planet was too far from the colony to cause danger).
I like the idea of bacteria myself. Bacteria can do lots of interesting things, and the activities of the colonists might disturb them and feed them. What if the bacteria are not inherently harmful, but given the presence of something the colonists bring with them, they mutate into something nasty? Brain eating bacteria? A weird disease? Who knows? More interesting: an alien race was going extinct. They didn't have the technology to leave their planet, but they had advanced genetic technology. Before they all died out, they encoded specialized viruses to lie in wait until some other life form came, and then penetrate that life form's genetic code and mutate them into the aliens? Sort of a genetic cuckoo effect.
The planet's internal composition is such that the magnetosphere changes periodically, much like how Earth's magnetosphere has undergone geomagnetic reversal in the past, indeed we seem to be due for another such event. A sudden reduction in the magnetosphere could result in increased surface radiation and would likely damage any electronics that aren’t properly shielded, satellites and spacecraft could also be affected.
This may not kill people outright (although the risk of sunburn and skin cancer will be greater) but for a fledgling colony losing all electronics and orbital infrastructure would be a devastating blow.
I think the best example of this was the planet "Eletania" in the Mass Effect series:
Eletania appears to be a world eminently suited for colonization. Sadly, appearances are deceiving. It is covered by a verdant carpet of mosses, algae, and lichen, and possesses a thick oxygenated atmosphere, but the animal kingdom is a web of microscopic symbiotic creatures. These are impossible to filter from the air and necessary for the native life to thrive. Unfortunately, they also cause anaphylactic shock when inhaled by non-native life.
In short, settlement requires either fully sealed environment suits, or replacement of the entire world’s ecosystem. Some have proposed limited colonization at altitudes above the symbiotes' range, or in areas where favorable winds keep the air clear.
I think dunc123 is more on the right track--we need to be looking for something the survey crews couldn't see.
However, I disagree with him about a pulsar in a nearby system--it should be obvious and how would it keep striking?
Instead, lets look closer at hand--there's a black hole in a distant orbit about the star, well out there in the Oort cloud. It was missed because it's small. (Formation means unknown. Once formed it's stable but we don't have any mechanism for them to be formed. Perhaps this is an alien weapon system??)
One pole is currently pointed towards the inner system. If there's nothing around it the black hole is quiet and all but impossible to detect without an extensive period of mapping orbits to find it's effects. However, sometimes it encounters something out there and when it does so the results are dramatic--including a very deadly radiation jet from it's poles. (Infalling matter sorts itself out into a disc which ends up absorbing any energy released in the plane of the disc, the energy that gets out is to a large degree normal to the disc.) The planet catches enough of it to devastate a terrestrial ecosystem. (There may be local life which has evolved to deal with the radiation storm. Unless the survey crews specifically test that local life for radiation hardness they're not likely to notice it.))