Based on the novella Het Gouden Ei by Tim Krabbé, The Vanishing begins with a glimpse into the life of chemistry professor Barney Cousins (Jeff Bridges) who is at his cabin trying to perfect the method to carry out a perfect kidnapping. He is so absorbed by this that his family, wife Helene (Lisa Eichhorn) and daughter Denise (Maggie Linderman), believe he is having an affair.
The film then cuts to vacationing couple Jeff Harriman (Kiefer Sutherland) and Diane Shaver (Sandra Bullock). They pull up to a gas station and Diane goes to the bathroom and never comes back. Jeff waits and goes to look for her but she is gone!
Three years later, Jeff is still obsessed with finding out what happened to Diane and is posting fliers and following leads relentlessly. He stops at a diner and meets a waitress named Rita (Nancy Travis) who looks after him.
One year later Jeff and Rita have settled in an apartment in Seattle. Jeff, who is attempting to write a novel, meets with a publisher who suggest that he write a book about the disappearance of Diane. Knowing this will upset Rita, he hides his project, buys a used military uniform at a surplus store and uses army reserve drills as a cover to continue his search.
One weekend, Rita is at home and curious about his project. She goes to the computer and cracks a code using several letters of Diane’s name, accessing Jeff’s rough draft of a children’s book. After reading it, she discovers it’s actually about Diane’s disappearance. Rita tracks Jeff to his motel room and angrily confronts him. Jeff finally tells the truth about how Diane disappeared and commits to only Rita. Following her ultimatum, Jeff abandons the search and burns the missing posters of Diane.
Months later Barney is on a University campus and discovers Diane’s missing posters covered with other fliers. He surmises that Jeff has given up his quest for the truth. He decides to bait Jeff by sending him a letter to meet him at a country club to learn the truth about Diane…