Notes:
- The game is non-linear, and certain events can occur before, simultaneously, or after other events. However there is a general progression through three main plot-lines as described below, even though the details will be different from one play-through to the next.
- There are a few ways to solve some of the puzzles encountered during the game (though most alternative "Solutions" only lead to more problems, or to a Non-Standard Game Over). This recap describes events as they will likely unfold during a Grand Strategic Victory, though there is no "canonical" storyline.
In the year 2043, Earth nations had been exploring the outer vestiges of the Solar system when a new comet was discovered arriving from the direction of Alpha Centauri. As it reached the Solar system, the "comet" turned out to be an alien craft, which destroyed the first American ship sent to meet it. Additional ships were sent to stop it as it plowed its way towards Earth, eventually releasing a swarm of missiles before finally being destroyed at great cost. One such missile managed to make it through the defenses, hitting Sudan and unleashing a virus that killed millions. This was the first strike in the Human-Centaurian war, which lasted a century.
The war caused the nations of Earth to finally unite into a global government under the control of the United Nations. The war effort produced many new technologies, including a Bussard collector that could fuel ships on interstellar journeys. This was eventually used to send an attack fleet to Alpha Centauri, which reached the system in 2132 but was destroyed. The Centaurians sent their own fleet to the Solar system, which in 2150 destroyed Earth.
Fortunately, the humans were prepared for this eventuality. Knowing that extinction was on the line, they used the Bussard engine technology to also construct 16 "seedships", sending human colonists in crygenic suspension to other potentially-habitable star systems, many lightyears away from Earth. Two such ships were sent to the Beta Caeli system: The U.N.S. Calypso in 2119, and the U.N.S. Tantalus in 2136. However, thanks to improvements in engine design in the intervening period, the Tantalus reached Beta Caeli 21 years before the Calypso.
The U.N.S. Calypso, carrying 2,000 colonists, finally reaches Beta Caeli. Automated systems on board the ship revive the ship's senior staff along with 50 colonists. The senior staff of the Calypso read messages sent from Earth some years after their launch, learning that another ship - the Tantalus - had been sent to Beta Caeli and was slated to arrive two decades earlier. However, no greeting is received.
The Calypso is found to be orbiting a terrestrial planet within Beta Caeli's "habitable zone". Although smaller than Earth, it is an ocean planet with land-masses and a similar atmosphere. It is named "Gaea" by the colonists, who proceed to set up a small colony on the surface and begin to produce the bare necessities for survival.
Astrometric observations performed by the ship's automated systems prior to arrival reveal information about the other planets in the system, showing that it is actually very similar to the Solar System:
- Planet Hermes, a mineral-rich planet close to the star, analogous to Mercury.
- Planet Rhea, a large habitable world that resembles what Venus might have become had it not undergone a greenhouse effect. It has a large moon called Prometheus, which is not unlike Earth's moon.
- The aforementioned Gaea, slightly colder and smaller than Earth.
- Planet Ares, analogous to Mars.
- Gas giant Zeus, with only two large moons (Hera and Hebe) and many tiny ones.
- Gas giant Cronus, similar to Saturn but missing any visible rings or moons.
- Gas giant Poseidon, larger than Uranus but with only one large moon dubbed Thetis.
- Planet Hades, with a highly eccentric oval orbit that periodically takes it from being the 7th and 8th farthest planet from the star, much like Pluto.
- A dense mineral-rich asteroid belt orbiting close to the star, dubbed Alpha: the remains of an ancient planet that had broken apart.
- An asteroid belt that failed to coalesce into a planet between Ares and Zeus, much like our Solar system's asteroid belt, dubbed Beta.
Plans are quickly drawn up to settle Gaea and Rhea. However, exploration of Gaea quickly turns up remains of the Tantalus colonies, and the sights are gruesome: all of the colonists are dead. As more and more information is collected, it appears that there was a massive battle between the colonists and the native wildlife of Gaea, even though the animals now appear quite docile and mostly harmless. Piles of animal bodies - sometimes thousands - are found just outside the remains of the abandoned colonies. It seems that even air-travel was unsafe, as aircraft were attacked by clouds of spores or flocks of bird-like creatures. Even more worrisome is the discovery that life on Gaea bears a strong genetic similarity to samples taken from dead Centaurians during the war.
Meanwhile, scientists on the Calypso discover that the cryogenic process they'd been put through for the journey may have negatively affected their DNA. After some intensive research, they discover a way to repair the damage, and in the process prolong the lifespan of the colonists by an indeterminate amount - possibly to the point of not aging at all. At the very least, this would allow the colonists time to establish themselves in Beta Caeli without the fear of growing old and dying before the task is completed.
After establishing a foothold on Gaea, the Calypso's on-board robotic assistant finally manages to reconstruct some messages sent from Earth that were poorly received in interstellar space, among them the final message from Earth indicating that it has been destroyed by the Centaurians. The Calypso settlers now realize that there will be no going back - Beta Caeli is their new home.
The Calypso finally makes it to Rhea and begins to establish colonies there. However, disturbing reports from Gaea begin to arrive: The animals are starting to attack the new Calypso colonists just as they had done to the Tantalus colonists. Meanwhile, additional exploration reveals that the commander of the Tantalus, Captain Johannson, had decided to dismantle the ship to use its fusion power plant in one of the colonies. Once the animal attacks began and the colonists could not easily escape, she was likely murdered by an angry colonist for that decision. The Calypso crew decide to keep their ship intact.
As the colonization effort proceeds, animal attacks begin to grow in intensity. At that point, exploration teams discover gigantic pylons of alien origin on the surface of both Gaea and Rhea. Records from the Tantalus colonies reveal that they found the same pylons but kept them a secret from the populace, and even blew one up just before the animals began attacking. It is theorized that the pylons may be directing the animals to attack the colonies somehow. The Calypso military advisor suggests destroying the pylons, but the science advisor suggests studying them instead. The pylons are left alone, but the animal attacks intensify even further. Fortunately, the humans quickly devise a force shield system that can keep the animals at bay, allowing the colonies to survive; but the resource cost of keeping the shields operative around each new colony are exorbitant, preventing further expansion. Efforts are redirected into building outposts on Hermes and the Alpha asteroids instead.
Eventually, a signal from outer space is detected being received by the pylons. Laboratories are set up on each planet, as well as in new space stations orbiting each planet, to triangulate the signal. It appears to be coming from the direction of the Beta asteroids, out beyond the orbit of Ares.
The Calypso moves to planet Ares to set up an outpost closer to the Beta asteroids, and begins to send unmanned probes to scout them out; however the probes' robotic pilots all suffer malfunctions and are destroyed. It is eventually decided to send human pilots who begin to scout the asteroids for the source of the transmission.
Eventually, the signal's source is traced to a hitherto-undetected new asteroid, dubbed Gamma 1. This corresponds to new information found on Ares indicating that the Tantalus colonists also discovered such an asteroid and proceeded to attack it with everything they had - unsuccessfully. The Calypso crew decide not to repeat that mistake, and instead to explore the new asteroid in person. They find more pylons scattered around it, as well as signs of ancient weapons on the surface that were mostly destroyed by the Tantalus attacks.
Before they can do anything about it though, the asteroid "comes to life", shedding its outer shell and revealing itself to be a ship. It powers up its engines and sets a course directly towards Beta Caeli. Fearing that the ship's engine would cause Beta Caeli to undergo supernova, the Calypso scientists scramble to find a solution to all of these rapidly-accumulating problems.
Meanwhile, exploration of the alien ship continues with urgency. A small incursion team finds an opening into the ship. Though finding no life inside, they do discover an alien data storage device which they bring back with them. Studies of the device reveal the history of the ship itself: It was built by an ancient race known as the H'riak, the first living species in the galaxy, formed billions of years ago. The H'riak found themselves to be alone, and therefore decided to seed as many planets as they could with life based on their own genetics.
The H'riak empire expanded throughout the galaxy, but then the Milky Way's core suddenly collapsed into a supermassive black hole (Sagittarius A*) - sending vast amounts of radiation in all directions, and destroying most H'riak worlds. In their desperation to ensure the survival of life in the galaxy, the H'riak apparently attempted to seed a gas giant with their DNA, but in doing so they inadvertently created their own worst enemy: a race of so-called "crystalline abominations" calling themselves "Empiants". For some unknown reason, the Empiants came out of their gas giant with a vengeance against their creators, sparking a war between the two species. The Empiants quickly multiplied, colonizing other systems and eventually surrounding the remaining H'riak worlds on all sides. During the war, an automated H'riak sporeship arrived in Beta Caeli and seeded it with life, implementing special genetic codes that would allow the local species to rise up against the Empiants on command. Though the H'riak eventually went extinct, this sporeship remained dormant and hidden in the Beta Caeli system, and is now sending that attack signal.
Using this information, the Calypso scientists develop technology to muffle the signal, which is hastily installed onto Gamma 1, stopping the animal attacks on Gaea and Rhea. On the other hand, the sporeship passes within close distance of Ares, and small fragments of its former asteroid disguise begin to shower the new colonies on the planet, forcing the engineers to invent and install an anti-meteor gun before they can be destroyed. Nevertheless, work continues on developing a massive fusion bomb to destroy Gamma 1 itself. Research and development of the weapon conclude shortly before it reaches Beta Caeli, and the sporeship is finally destroyed with minimal damage to the nearby colonies.
With the Gaea, Rhea and Ares finally saved from certain destruction, the colonists begin the arduous process of constructing space stations around the three gas giants in Beta Caeli, with a mind to siphon their upper atmosphere for nearly unlimited amounts of energy. Probes are also sent as far as Hades, discovering that the Tantalus colonists did manage to set up colonies that far out in the time they had. Unfortunately, none of them survived once the Gaea and Rhea colonies fell; Many committed suicide.
Not long after setting up the first siphoning station around Zeus, however, the Calypso network is hacked by an outside force - jellyfish-looking purple aliens, speaking in an unknown language. While scientists work on trying to decypher it, the aliens contact the humans several more times. Then, suddenly, a force of alien spacecraft come flying out of the atmosphere of Cronus. With one last message, the aliens begin to attack the humans in space. It is quickly realized that the aliens have a tremendous telepathic power - so strong that it can cause the heads of human pilots to explode from a great distance.
Thoughts arise about creating another fusion bomb to destroy the alien civilization on Cronus, but the Calypso's captain decides to continue the research instead while fighting a defensive war. Eventually, the scientists develop a device called the "Alpha Enhancer", which allow humans to send and receive telepathic signals - theoretically enabling direct communication with the aliens without the need for translation.
Once the technology is ready, it is quickly discovered that the enemy race is in fact the Empiants. They indicate that the reason they attacked is because the humans are hurting them with their thoughts. As the Empiants intensify their attacks towards Gaea and Rhea, the Calypso scientists quickly develop a device that softens telepathic signals. It is dropped onto the solid core of Cronus.
The Empiants thank the humans for stopping their pain, and immediately declare an end to the war. They quickly turn out to be a very helpful and friendly species, asking only that the humans do not siphon energy off their planet's atmosphere. However, they agree to allow the humans to keep a station around Cronus. They even offer a scientific collaboration on the Cronus station. Per their request, the human colonies soon begin delivering massive quantities of resources to Space Station Cronus, setting up advanced laboratories according to the Empiants' exact specifications.
Finally, the Empiants contact the humans and make a keen observation: The Beta Caeli system is short on mineral resources, and before long the humans would need to escape it and find someplace else. With resources on Ares and Hermes already starting to dwindle, the humans agree to this assessment. Fortunately, the Empiants propose a plan: Create a method of Faster-Than-Light travel, based partially on Empiant telepathic abilities. They claim to have the know-how, but lack the technical ability of the solid-world humans to build it. The plan would involve the creation of a massive structure out in space, which could propel an Empiant-operated ship to other star systems. The Empiants do not fully explain the process by which this is achievable, but provide precise blueprints for the creation of both the superstructure and the new ship.
Work on the project begins immediately, at a site known as "The Superstructure" out near the orbit of Zeus.
Word soon comes down that one of the planetary governors, a woman named Bach, has begun an insurrection among the colonists. She has stoked fears about collaboration with the Empiants, and has brainwashed her followers into abandoning their colonies and raiding them for equipment. Using stolen ships, these fanatical rebels begin attacking the Empiants. Despite all of their wisdom, the Empiants are incredibly intolerant to disorder, and this act severely threatens the peace treaty.
Bach soon announces that the rebellion has chosen a site for a new colony on Hermes, which they name "Persephone". She demands that the colonists build enough space for all thousand rebels to live there. She threatens to make a massive missile strike against the Empiants if they fail to comply. It is clear that Bach is hoping to set up her own little empire on Hermes. In a private message to the captain of the Calypso, Bach reveals that her actual motives are quite selfish and extremely megalomaniacal; She is resentful that she was passed over to command the Calypso, and wishes to humiliate the current captain. In her insane delusion, she believes she can convince the (long gone) United Nations that she had been the right choice for captaincy all along, and that they would appoint her the new leader of the colonies.
With no other choice, the captain orders a construction project be started, but simultaneously orders scout ships to scour the system in search of Bach and her converts. This begins a wild goose chase, in which clues intentionally left behind by Bach at various fanatic outposts lead the scouts to many dead ends. Nevertheless, she is eventually tracked to Hades, where the Calypso scouts find a bunker system protected by many stolen weapons. With many innocent, brainwashed civilians inside, the Calypso military decides not to attack.
Finally, enough habitats are constructed at Persephone for all 1,000 rebels. Rebel shuttles from all across the system begin to congregate at Hades, where they group up for the flight to Persephone. Shortly after they leave, a message is intercepted: Governor Bach's shuttle has failed to take off from Hades, requesting her followers come pick her up. Before they can do so, Calypso scout ships manage to reach Hades and destroy the bunker. The colonists are taken to Persephone to be "de-programmed" and returned to their old lives in the other colonies.
With the rebel threat finally over, the massive Superstructure project can continue, depleting most of the resources of the Beta Caeli system. Nevertheless, a gigantic ring structure is created, with four towers along its edge pointing inwards at its center. Work also concludes on a new ship, adapted for co-habitation by both humans and Empiants.
Finally, the ship is manned by members of the second generation of humans, born in Beta Caeli, together with their Empiant counterparts. The Empiants aboard focus their telepathic abilities to create a sort of "lens" at the center of the ring. The ship flies into this lens, and is propelled away from the system at immense speed.
The members of the first generation of humans - those who personally arrived in Beta Caeli with the Calypso - stay behind to live out the rest of their days there, however long that might be.
