Full Lore

The Fleet
The ESS ELYSIUM and ESS TRITON were a research fleet travelling together. The ESS ELYSIUM was designed to research the LRDs, and the ESS TRITON was researching the Galastropods, added in the Xenobiology Update. When a LRD upon the ELYSIUM had driven Dr. Stone, a researcher upon the Elysium insane, disaster struck. Dr. Stone had sabotaged the Elysium, crashing it into a nearby planet. Before the Elysium crashed, the ship's AI helper, Chronos, uploaded the Mind-Banks of every crew-member into the Astroneer Training Program in an attempt to save them.

The Simulation
Chronos had loaded himself into the Control Room of the simulation, giving him full superuser access. The simulation only held data for one system, the Sylva System. Despite the power of the 25th century tech, the Astroneer Training Program fell unstable with every crew-member loaded at once, so Chronos had to instance the Astroneers. This is why we do not encounter other crew mates. Upon the crash of the Elysium, the simulation sustained critical damage and began to corrupt. Planet data began to destabilize, removing features that in the real world would normally be present. Three of the crew-mates became corrupt and their memories were scattered on Vesania, Calidor, and Atrox. Chronos had began to slowly corrupt over time, so he had to find a way to save the crew in time, but he was unable to communicate with the crew, so he had to manipulate the simulation to help them.

The Rifts
In the simulation, there are some instabilities that cause rifts to appear. At the end of the Rails mission, we can see that Bell slips through a rift into our instance momentarily before being pulled back into her own.

The S.O.S.
At this point, Chronos had formulated a plan to save the crew; Send an S.O.S. signal to EXO Dynamics. As a fail-safe, Chronos built EVA, A fox-like companion to aid an Astroneer in sending the signal in case Chronos failed. Chronos had disguised the communications modules in each instance as the ancient structures on Novus so that Astroneers would power them inadvertently. The ancient structures appeared to be giant teleportation structures located on the Surface, Core, and as a giant sattelite. Eventually, the player activates every "Gateway Engine" and finishes every priority mission.