At a Catholic boys' school, domineering disciplinarian Father Goddard rules over his pupils with an iron hand. When one of his teenage charges confesses to murder, the dogmatic but deeply repressed Goddard finds his faith challenged and his life spiralling dangerously out of control.

Omega, an ancient Time Lord made of pure anti-matter, once defeated by the Doctor, is plotting to cross over into this dimension by bonding with the Doctor. Meanwhile, the disappearance of a man in Amsterdam piques the curiosity of his cousin, Tegan, who previously left the Doctor at Heathrow Airport and now finds herself at Omega's mercy. Fearing total destruction from the collision of matter and antimatter, the Time Lords recall the Doctor to Gallifrey to undertake the only viable solution: executing him!

For various reasons, a number of people have come see the painting Water Lilies by Claude Monet in the Museum of Modern Art in New York. Two businessmen caught up in office politics discover the truth about themselves and their situation. Angie and Marcia, two elderly matrons, find a place to rest their weary feet. David, a shy English student, meets a young student museum guide, and a married couple find the peace of the room gives them the strength to talk truthfully about their relationship.