Full Lore

The Rescue
The ESS Triton (Captained by Xenobiologist Dr. Iness) was investigating an anomaly with Galastropods and LRDs onboard when presumably a crew member went insane due to studying the LRDs and nearly destroyed the whole ship before Dr. Iness could jettison the lab to save the Galastropods. In response, Dr. Iness's brother, Chronos, who is also an AI Companion of the ESS Elysium, sets out with his research crew to rescue Undine. Upon reaching the Triton, an onboard LRD: Zebra had hypnotized a crewmate into sabotaging the ship, causing it to fall towards a nearby planet. Before planetary impact, Chronos had made an attempt at saving the crew by uploading the crew's Mind-Banks into the Astroneer Training Simulation.

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 in-game. 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.

Background Info: Chess Pieces
Chronos claims that upon corruption of a crewmate, he could have sworn that he saw miniature statues on both moons resembling the pieces of the corrupted crewmate's chess set.

Background Info: Galastropods
Upon loading the crew into the ATP, data from the Triton consisting of the evacuation protocols and Galastropod data was integrated into the simulation. This causes Galastropods and Xenobiology logs to appear inside the simulation as well.

Background Info: 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 (The Conductor) slips through a rift into our instance momentarily before being pulled back into her own. This also occurs when completing the Vintage Probe mission, where Bert takes our picture before leaving.

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 satellite. Eventually, the player activates every "Gateway Engine" and finishes every priority mission. By this time, enough gateway engines are activated to send the S.O.S., but Chronos is already corrupt by this point. This gives EVA the signal to begin directing you into finding her.