The story takes place 500 years after humans first ventured outside of the
Solar System. The Beta (or
Mora, as they call themselves), a once-spacefaring culture, has fled with the remainder of their civilization to Ecosystem 9 (which they call
Falkannan), the planet the game takes place on, from an unknown threat they call the Silent Ones. During a test firing of the
wormhole they meant to use to return to the stars, they are attacked by enemies coming through the portal, or "Keyhole". These advanced
drone units are first suspected to belong to the Silent Ones but are later revealed to be human in origin. As the conflict between the Beta settlers, led by Aran (Commander) Saruk, and the human forces intensifies, an explosion in orbit scatters wreckage all over their colony, from which the
Goo emerge and attack both sides. After a long history of war and exploration in space, during which no intelligent life was found, humans had returned to planet Earth in an attempt to seek peace and stability in a
post-scarcity society guided by
AI. A signal is detected from the distant planet Ecosystem 9 in the outer
Crux Arm, and the starship
LSV Darwin, captained by Lucy Tak, is sent to investigate. Landing forces are engaged by the Beta (who are designated as such by the humans because their original planet was the "beta candidate" for intelligent life during previous
radio telescope surveys, but subsequent investigation did not receive any more signals — likely a consequence of the Silent Ones' attack) and collect samples from the surface, including Goo, which promptly escapes and destroys the
Darwin, reaching the Beta colony site in the re-entering wreckage. Despite their initial conflict, the Beta and the now-stranded humans agree to an alliance to destroy the Goo that threatens them, which is revealed to be part of the artificially intelligent "
Pathfinder"
Von Neumann probe system sent from Earth centuries prior to chart the galaxy in advance of the human expansion. The probes were believed to have been decommissioned when exploration was abandoned, but presumably the Goo on Ecosystem 9 somehow altered its own programming, becoming self-directing. After sacrificing himself to destroy what was believed to be the last Goo on the planet, the robotic human commander Singleton's consciousness merges with the Goo. It is revealed that the Goo are attempting not to consume life, but rather to protect it from "the growing shroud of Silence" that is expanding across the
galaxy — the same unknown force that destroyed the Beta civilization. All previous hostile actions were merely attempts to expand in order to effectively defend the planet. With Singleton's assistance, the Goo fights back from the brink of extinction and carves a path to the Beta's Keyhole device in the hope of contacting and reuniting with the scattered Goo across the galaxy, to stand united against the Silence. Singleton attempts to negotiate with the Humans and Beta, but the Goo is forced to destroy the opposing armies. Defeated, Saruk, Tak and others who were spared watch as countless Goo masses emerge from Keyholes across the planet. In an after-credits scene it is hinted that the "growing silence" has discovered Ecosystem 9. In the 'Descent of the Shroud' update, the "growing silence" was revealed as the newly added fourth playable faction, the Shroud. ==Release==