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Mysteries are in-game storylines that usually contain a potentially harmful or alien element. Mysteries start between 1 and 15 Sols after certain requirements are met. Every Mystery will grant a random Wonder technology if successfully completed. If all Wonder technologies have been researched the Mystery will grant a Breakthrough instead. Mysteries are different from Story Bits, which involve simpler storylines and options.
As of the Green Planet DLC, there are 12 mysteries in the game.
Between 10 and 30 Sols after the Marsgate trial if you exposed EsoCorp you will be notified that EsoCorp rovers are approaching Mars and gain access to the inexpensive Defense Turret Breakthrough. A few days later the first wave will arrive and EsoCorp rovers will descend all over the map. They will advance towards the colony and bombard anything within range with missiles, while Defense Turrets will counter them. It should be noted that Defense Turrets have greater range than EsoCorp rovers. The maintenance bar will act as a health bar. Once the first wave will be destroyed the second wave will approach but you will be notified that destroyed EsoCorp rovers can be repaired and used or salvaged for resources. Once the second wave is destroyed the Mystery ends and you will gain the random Wonder or Breakthrough technology.
The Last War Mystery features a mechanic called War Tension which measures how close the war on Earth is from becoming a nuclear war. It starts at 10%, increases at a rate of 1% per Sol and can be increased or lowered by Mystery choices. Within 15 Sols, resupply of resources will be cut off until the Mystery ends. There are three possible outcomes of the Mystery depending on War Tension:
If War Tension is reduced to 0% the war ends with peace treaties. (random Wonder or Breakthrough technology, 50 Applicants, -50% Resupply costs)
If War Tension doesn't reach 0% or 100% after 100 Sols, the war will end with the Second Cold War. Resupply becomes available but costs are increased by 50% for 50 Sols.
If War Tension reaches 100% a nuclear war will devastate Earth. Export, Research Outsourcing and Resupply will become unavailable. 50 Sols later contact with the remaining humans is reestablished. Rockets become available again.
Wildfire features a mechanic called Infection Level which measures how close the infection on Earth is from eradicating all humans. It increases every time an Earthsick Infected colonist leaves Mars and is reduced every time a Rocket loaded with the Wildfire Cure is sent to Earth. It goes through 5 levels, with the following effects:
Contained - initial stage
Endemic - export prices increase
Epidemic - applicant pool depleted
Pandemic - resupply costs increase
Extinction - most of Earth's population is dead and Export, Research Outsourcing and Resupply will become unavailable. 50 Sols later contact with the surviving humans is reestablished and Export, Research Outsourcing and Resupply become available again.
When Metatron opens communications with the colony it presents a challenge to you; prove that humanity has the curiosity and ingenuity to survive in the galaxy. Its first task for you is to solve a series of timed anomalies; two rovers on automated mode can take care of this, so it's recommended that you order these from earth as soon as Metatron arrives. After a few waves of timed anomalies it moves on to ion storms, an artificial disaster that disables all out-dome buildings within a certain radius; it sends up to five of these at once and continues for several sols. Once you research the ion storm prediction breakthrough it eventually gives you its final challenge, construct project morpheus within twenty sols. You are given the technology, all you need to do is build it. The most reliable way to get enough electronics in time is to import them; the metals and concrete are easy enough. Once project morpheus is complete Metatron disappears and you are given the random wonder/breakthrough tech.