Signalis

Signalis takes place during an era with space travel and advanced technology, in an unidentified planetary system that is governed by the totalitarian Nation of Eusan, which remains at war with a larger Empire that it broke away from. The political and economic center of Eusan is the Rotfront colony, but it maintains outposts on other nearby worlds. Eusan employs Replikas, androids made with copied human neural imprints, as the bulk of its military and labor force. A consequence of using neural imprints is that Replikas inherit various idiosyncrasies from them, such as a compulsive desire to listen to music or bathe, and failure to indulge these idiosyncrasies can cause a Replika to destabilize and cease functioning. Human commanders called Gestalts manage and give direction to Replikas.

A Penrose-512 scout shuttle is crashed on an unknown planet. A Replika unit known as Elster (LSTR) awakens and searches for her missing Gestalt partner, Ariane. She eventually goes out of the ship, where she crosses a rectangular arch. She finds herself in front of a hole containing a staircase. Once she descends, she crawls into a tight flesh-like tunnel leading into a room, as the hole closes behind her. As she picks up a book called The King in Yellow, the radio turns on and a broadcast of numbers is read in German, all the while the quote "Great holes secretly are digged where Earth’s pores ought to suffice, and things have learnt to walk that ought to crawl." from H.P. Lovecraft's The Festival is shown. The broadcast ends on visions of Ariane and some text asking Elster to "Remember our promise" and "wake up".

Elster suddenly finds herself in the Sierpinski-23 mining facility located on the planet Leng with a photograph of a woman named Alina, who resembles Ariane. She quickly discovers that most of the Gestalt staff is dead and the Replika workforce has gone rogue, somehow having turned into hostile, mindless beings that attack her on sight. Elster begins to explore the facility, gathering supplies and looking for clues about what happened and where Alina may be. She then encounters the facility's Replika administrator, Adler, who pushes her down an elevator shaft. Elster lands on dozens of bodies from other LSTRs, but survives the fall. She then continues her search, finding Adler's diary which indicates he is able to recollect memories he didn't live, which he believes originate from other realities. Elster delves deeper into the mines below the facility, finding that the lowest levels consist of a gigantic mass of flesh, and goes through a door that leads to a threshold identical to the rectangular arch in the opening. Adler despairs about the fate of Falke, the commander of the facility, who had changed when she came back from beyond the arch and never explained what she had seen. Elster crosses the threshold and finds the Penrose-512, but accidentally tears her own arm off attempting to open the airlock and subsequently passes out. Other LSTRs bodies can be seen.

While unconscious, Elster has a dream about Ariane, which portrays a happy memory between the two in which they end up dancing after embracing each other. After this dream, Ariane is portrayed standing above Elster, asking her if she remembers their promise. Elster regains consciousness and manages to reenter the Penrose-512, scavenging parts from another dead LSTR unit to repair herself. She then jumps down a hole that has appeared in the ship and find herself back in Sierpinski-23, in the same room she first was, though the environment has become inundated with masses of flesh. Making her way through the facility, Elster drops down another hole and somehow finds herself in the colonized moon Rotfront. There, she learns that Ariane was relentlessly bullied by her classmates and signed up to be a Penrose scout pilot to escape her torment. Elster continues on as the environment becomes more surreal and she encounters the Replika Falke. Various collected notes reveal that Falke has inherited Elster's memories and now has a crisis of identity, leading her to attack Elster.

Elster is able to defeat Falke, who states that "we are one" as flashbacks of both Elster's and Falke's memories after her interaction with the Penrose-512 are shown. She then returns to the threshold where Adler is waiting for her. Adler warns Elster that no matter what she does, once she crosses the threshold time will loop again, reality will fall apart, and that it could shatter at any time. Elster continues anyways and a scuffle ensues, with both Replikas being mortally wounded — Adler is shot and Elster is stabbed in the eye. Elster continues on and returns to the wreckage of Penrose-512, where it is revealed that if the scout pilots failed to find a habitable planet, they were not expected to return home. Eventually, the radiation shielding failed and Ariane was afflicted with acute radiation poisoning. Another note reveals that about 5400 cycles into the mission, Ariane wished nothing but to die.

Depending on Elster's actions throughout the game, four endings are possible:

• To acquire the "Leave" ending, the player must be conservative with ammunition, heal frequently, and spend a long time exploring. In this ending, Elster cannot work up the courage to see Ariane again and carry out their promise, instead leaving the ship to succumb to her wounds in the wasteland outside.
• To get the "Memory" ending, the player must utilize a balanced playstyle. Elster awakens Ariane, but she doesn't remember who Elster is nor their promise. Elster cannot follow through with the promise and stays by Ariane's side until she succumbs to her wounds.
• The "Promise" ending requires the player to play aggressively, killing numerous enemies, dealing a significant amount of damage, and spending a long time in the game. Elster awakens Ariane, who remembers her and asks her to keep their promise. Elster reluctantly follows through, killing Ariane before succumbing to her own wounds.
• In the secret "Artifact" ending, after acquiring three hidden keys throughout the game that unlocks Ariane's safe which yields a vase of white lilies, Elster performs an esoteric ritual that results in her apparent death. A memory of her and Ariane dancing can then be seen inside the wreckage of the Penrose-512.

It is to be noted that a significant part of the plot is left up to the player's interpretation; while some theories are more accepted than others, there is no single consensus about the whole story.