Differences between Original and Director's Cut versions
A narrative is added to the game, in the form of non-interactive voiceovers told to the player between puzzles, written by Rob Yescombe. To accommodate this, a number of elevators have been added between sectors and in other locations, and existing elevators are often slower. Several other cutscenes are also slightly altered to better support the plot. Cutscenes can now be paused on the PC with the escape key, but still not skipped. The game includes a new music score.
Although the majority of puzzles remain unchanged, several are modified or rearranged and a small number are removed entirely. The most changes occur in a 'dark' sector, which is directly shortened by the removal of the most difficult puzzles. Many puzzles using wires have been re-designed or altered to make the wire behavior more consistent. Hidden puzzles were already in some map areas, but at least one more has been added. Additionally, the player's progress (shown for a portion of the game on a light-up 3x3 board) is now shown on a 2x3 board.
Graphical features have been improved, including the addition of fire and smoke effects. However, the PC version has fewer audio sliders - where the original had separate settings for master audio, music and sound effects, the Director's Cut retains only the master slider.DLC for the previous game - a "race against the qlock" time trial mode - and Oculus Rift support are also included in the Director's Cut.
Warning: Spoiler warning!
The player wakes up in a featureless room built of cubes, and is quickly contacted over their suit radio by a woman who claims to be alone on the International Space Station, talking to them on behalf of Mission Control. She tells the player they are far from on Earth on an alien structure that threatens the planet, that their mission is to prevent that from occurring, and the amnesia they are likely suffering is a side-effect of the space travel. The woman only contacts the player occasionally and never for long, supposedly due to line-of-sight blockages as the ISS orbits the Earth.
As the player travels through the structure, they are contacted by another person - a man who identifies himself as "Number 919" - who claims the player is in reality in an underground testing facility, he is also trapped alone somewhere, and that the woman is lying to him. The two broadcasters can hear each other; the woman later claims the other is Jonathan Burns, an astronaut from the lost space shuttle #919 (and long presumed dead). The man instead suggests this name is a threat - that the player's own name is Jonathan, and he will be burned to death when they are done testing.
The man continues to convince the player that he is right and the woman is lying, including making self-referential comments about the game design (such as purely decorative destruction, linear pathways, and the presence of human symbols). Alternatively the woman regularly makes promises of further contact with Mission Control, the player's wife, and eventually "the President", also talking to the player about the pschological dangers of being alone for long periods and their own experiences of that on the ISS. Contact with others is continually delayed and postponed.
Eventually the player reaches a large room with what the woman claims is an escape vehicle, situated at the top of a near-endless downward pointing tunnel. The man instead claims this will take him to his death further underground. The player has no alternative but to eventually board the vehicle, while the man continually begs him not to go.
The ending cutscene reveals that the woman was correct - the player has been ejected safely into space, with the alien structure breaking apart near the Earth's moon. Though conversation remains one-sided, outside contact is finally made - first with Mission Control, then the player's wife and finally the President. The latter then tells Jonathan Burns and assures him he will soon be rescued too.