The book is set in 1954 and revolves around the life of U.S Marshall Teddy Daniels, as well as his partner, Chuck, as they travel to Shutter Island, a home for the criminally insane. One of the criminals imprisoned on the island, Rachel Solando, has gone missing, and they are attempting to find her.
As they are investigating, Teddy comes to suspect that there is one more person on the island who is not meant to be present. They also discover that psychotropic drugs are being tested on the criminals. Teddy is desperate to find the missing criminal, and speaks to an inmate who tells him that he should not trust Chuck.
Teddy then learns of a woman claiming to be Rachel Solando who is hiding out in one of the caves. She reveals that his food and drugs have been spiked with the psychotropic drugs. He then tries to find Chuck, who is missing. He then heads off to the lighthouse, where he believes the experiments are being conducted on the criminals.
He then finds Dr. Cawley, who tells Teddy that he is in fact Andrew Laeddis, and that he has killed his wife, Dolores Chanal (an anagram of Rachel Solando), after she killed their children. Chuck arrives and it is shown that Chuck is actually Dr. Sheehan, his psychiatrist. Sheehan claims that he and Dr. Cawley have given Andrew/Teddy the drugs to help him live his fantasy out in his mind and ultimately confront the truth about how he killed his wife. If he doesn't accept the truth, the doctors will force him to undergo a radical lobotomy.
The ending remains ambiguous as to which is the true version of events. Is Teddy really Andrew, and if so, is this the truth about his past, or merely another fantasy?