The game takes place in 1984 in a fictional Shropshire village named Yaughton. The player's objective is to explore and try to discover how and why everyone in the village has disappeared. Mysterious floating orbs of light swim around the air and lead the player to scenes made up of other human-shaped lights, which re-enact various previously occurring events.

Following the orbs' evidence from scene-to-scene across the valley, as well as finding telephones and radios that replay conversations, recordings, and broadcasts, eventually provide all of the puzzle pieces to the game's main event, the "rapture". There are five areas in the game, each of which revolve around a different character, with the main protagonists being Dr Katherine "Kate" Collins and her husband, Stephen Appleton, both scientists at the observatory.

During their work, Kate and Stephen encounter a strange pattern of lights in the night sky which they believe is an unknown form of life. They observe the pattern infecting and sometimes killing other lifeforms such as birds and cows, before spreading to humans. Kate concludes that the pattern is attempting to communicate with humans, ignorant to the harm that it is causing them. After confronting Stephen about his ongoing affair with his former fiancé Lizzie Graves, Kate locks herself in the observatory and spends the vast majority of the story attempting to communicate with the pattern.

During this time, Stephen becomes convinced that the pattern is a deadly threat capable of destroying the human race. Most of the valley's inhabitants begin to succumb to symptoms of unexplained hemorrhaging; pressure in the brain that is normally consistent with a brain tumor, as the doctor notes in a left-behind recording. Other people disappear, leaving behind a room full of odd specks of light and the lingering scent of unidentifiable ash. Convinced that this is connected to the pattern and that it will spread beyond the village if not contained, Stephen urges the local government to quarantine the area, blocking the roads and cutting the telephone lines.

The locals are told that it is due to an outbreak of Spanish flu, though many are skeptical of this and become even more so when the corpses of the dead begin to disappear into thin air. As the town's population rapidly dwindles, Stephen realizes that the quarantine has failed and that the 'pattern', or 'It' as it is often referred to, has learned to adapt. He believes that it has learned to travel not just through direct human contact, but through the telephone lines, radio waves, and television sets. In light of this, he desperately insists to the local government that they must gas the valley.

In the penultimate chapter of the game, the player is led to a bunker where Stephen waited out the nerve gas bombings with the intention of killing himself once he ensured that every other infected person in the valley is dead. When he is unable to reach anyone at all outside the valley via telephone, he realizes that he has failed and that the pattern has spread, presumably to the entire planet. The pattern comes for him and he confronts It. He tells It that he has decided to set fire to himself, having doused himself in petrol to prevent being taken by It.

Moments before he ignites the fuel, an image of Kate appears in the pattern of the light. Stephen stands in awe, reaching out to her. The scene fades out as Stephen's lighter slips out of his hand and hits the ground, igniting the petrol. In the final part of the game the player is transported to the inside of the observatory's locked entrance gate. The player makes their way up the hill to the top-most observatory and upon entering, sees the human light shape of Kate inside in the darkness, making the last of the recordings heard.

She states that she is the last one left, and it is revealed that she did achieve communication with It. Kate explains that when she told the pattern that what it did to everyone in the valley - the people, the birds, the insects, the cows - was wrong; It countered that it was not wrong, because now everyone that wanted to be together was together, and that everyone had found their counterpart and was no longer alone.

Kate explains how she finally understands and says that she has accepted her fate, and that she and 'the pattern' will soon join the others. She states that humanity can finally 'slip away, unafraid.' Kate turns and appears to reach out to the pattern coming down from above as it reaches out to meet her, her last words being her belief that the pattern was her own counterpart.