Emily Rutherford and Tom Charrington meet with a representative of Separation Day Incorporated to arrange their Separation Day. As their respective IQs differ by more than fifty points, they are not allowed to marry or have children. Separation Day Incorporated will provide for them the perfect place for them to make their farewells.
They spend one last week together before their Separation Day, then go to the station where a simulation of the library in which they first met has been prepared for them. However, as they prepare to say goodbye, strange things happen. Words in books change, a moth explodes in midair, and the bookshelves ripple. A statue of two lovers starts to come alive, and a loud groaning sound is heard, accompanied by the appearance of a large blue box.
The two people who come out of the box introduce themselves as the Doctor and Sarah. The Doctor tells Emily and Tom that they must not separate: the fate of the universe depends on their staying together.
As conditions in the library worsen, the group huddles near the TARDIS while the Doctor explains that Emily and Tom's separation will set in motion events that will eventually result in the destruction of the universe. The strange happenings in the library are the universe's way of trying to warn them.
Suddenly, the Director of Separation Day Incorporated appears, but he starts talking strangely. He starts to transform in horrible ways, and the Doctor convinces him that his only release is to enter the instability. The Director embraces the statue, and an explosion occurs that collapses in on itself. The Doctor now urges Emily and Tom to decide their future. They tell each other they will stay together; the library is restored to normal.
The Doctor explains to the others that Separation Day Incorporated is really a research project, probably sponsored by the government. The Director was a research organism, and as it absorbed so much grief from so many separations, it empathised with the clients.
Fifty years later, Emily reflects on the past few decades. About five years after the events in the library, government regulations had changed and Emily and Tom were allowed to marry. They have had a happy life, but they wonder about the Doctor and Sarah: were they just part of the universe's message, or were they really time travellers? Emily prefers the second theory.
- Emily was reading Pride and Prejudice by Jane Austen when she first met Tom.
- The statue in the library is a reproduction of Rodin's "The Kiss".
- George Orwell laid down eleven golden rules for the making of a perfect cup of tea.
- The Doctor name drops Lord Byron.
- K'anpo Rimpoche warns the Doctor of the Collision.
- The events that lead to the end of the universe are:
- Emily marries in twelve years and has a son named Daniel;
- Daniel is a bully who causes a fellow student to commit suicide;
- The suicide causes the resignation of a Professor Henderson;
- Henderson never works with Professor Mirsky;
- Mirsky invents a gaseous weapon called Close Gas;
- a terrorist group uses Close Gas, causing the deaths of schoolchildren in South Africa
- in retaliation, the weapons factory in Europe is destroyed;
- every nation on Earth becomes involved in the ensuing war;
- Vorlat ambassadors are killed in the fighting;
- the rest of the Vorlats become involved in the war and are destroyed, so that they cannot mediate in the dispute between the Malorians and the Vulzene;
- the ensuing space war is eventually joined by the warlike Jesh;
- the Shandance try to intervene in the war but are confronted by the Jatiri;
- the clash between the Shandance and the Jatiri, known as the Collision, lasts one day and destroys the universe.