Amos Trenoweth of Lantrig in Cornwall has to leave the country following the death of a preventive officer in 1794. He meets Ralph Colliver and falls in love with Colliver's fiancée. Amos and Ralph become pirates and discover the 'Great Ruby' of Ceylon in the possession of a Buddhist priest at a temple below Adam's Peak in Ceylon. In April 1805, to obtain sole possession of the ruby, Amos murders Ralph Colliver in the presence of Colliver's wife. Mrs. Colliver is six months pregnant with Simon, but Simon is not informed of the murder of his father and the loss of the Great Ruby until 1815.
Amos leaves instructions regarding his treasure with Mr. Elihu Sanderson of Bombay. He returns to Cornwall and buries the treasure at Dead Man's Rock, below Lantrig. In 1814 he settles back at Lantrig, being now a convert to Methodism, and marries Philippa Triggs of Mullyon. Ezekiel is born to Amos and Philippa in 1815. On 15 June 1837, Amos visits his attorney in Plymouth, where he is recognised by the clerk, Simon Colliver, as the murderer of Ralph Colliver and the possessor of Ralph's treasure. Amos dies on 27 October 1837, leaving Ezekiel with his will and the name of Elihu Sanderson of Bombay.
Ezekiel inherits Lantrig but gradually falls on evil times. No longer able to support the family, he decides in 1848 to sail to Bombay in the hope of contacting Elihu Sanderson, as instructed in Amos's will. While in Plymouth securing passage on board the Golden Wave, he is recognised by Simon Colliver who guesses Ezekiel's intention and secures berths for himself and John Railton on the same ship. Railton was a seafaring friend of Colliver's who had left the sea to run the Welcome Home inn with Lucy Railton, formerly Lucy Luttrill. Lucy is left in Plymouth with their daughter Jenny (or Janet Railton).
Simon Colliver and John Railton accompany Ezekiel Trenoweth to Bombay. As Elihu Sanderson senior is dead. Elihu Sanderson junior gives Ezekiel the envelope of instructions left by Amos and provides him with accommodation after Ezekiel is attacked from behind by John Railton. After recovering at the home of Sanderson, Ezekiel follows the instructions of Amos and makes his way to Samanala or Adam's Peak in Ceylon. He is tracked by Colliver and Railton. On 27 January 1849, Ezekiel reaches the place indicated in the instructions of Amos. He discovers the bones of Ralph Colliver and the priest; a 'Buckle of Gold' in two pieces, later called the 'Golden Clasp'; and a carving of the face of Ralph Colliver. The instructions inform Ezekiel that the secret of the Great Ruby lies inscribed on the two pieces of the Golden Buckle and on a key hanging from a beam at Lantrig. Putting the Golden Buckle'inside an envelope, he becomes aware of having been overlooked by Simon Colliver.
Returning to Colombo, he takes passage aboard the Belle Fortune, only to find Colliver and Railton as fellow travellers. Colliver manages to steal one piece of the Golden Buckle, thus obtaining half of the necessary information. Nearing the Lizard, Colliver and Railton organise a mutiny, only to have the Belle Fortune founder on Dead Man's Rock on the 12 October 1849. Railton murders Ezekiel Trenoweth with Colliver's knife and obtains possession of the envelope containing the second half of the Golden Clasp. A couple of hours later, Jasper Trenoweth, Ezekiel's son, meets John Railton on Dead Man's Rock, and is shortly afterwards joined by Simon Colliver. Railton slips Jasper the envelope before being murdered by Colliver. The sudden appearance of Dr Cyrus Loveday and a search party saves Jasper from a similar fate.
At the coroner's inquest on the afternoon of 12 October, Colliver pretends to be a Greek sailor from the James and Elizabeth, captained by Antonius Merrydew. That evening Jasper is threatened by Colliver through the window at Lantrig. Colliver then travels to Plymouth, marries Lucy Railton and escapes abroad before he can be apprehended by the law.
At noon on 13 October, the body of Ezekiel Trenoweth, with a tin box containing his journal, is discovered and carried to Lantrig. Margery dies of grief. Dr Loveday and Jasper Trenoweth find themselves in possession of Ezekiel's journal, half of the Golden Clasp and the key, all worthless without the second half of the Golden Clasp. Lantrig is sold and Jasper goes to live with Dr Loveday and Thomas Loveday, his nephew. On the death of Dr Loveday, Jasper and Thomas enroll at Guy's Hospital in London, in January 1863, Tom Loveday writes a play called Francesca: a Tragedy, which is accepted at the Coliseum Theatre, the lead role being taken by Clarissa Lambert (Claire Railton). Both Jasper and Tom fall in love with Clarissa, who had been forced onto the stage by Simon Colliver's mother.
On 9 May 1863, having little money left, Jasper and Tom enter a gaming hall with their part of the Golden Clasp and are recognised by Mrs. Colliver, who informs Simon. Francesca opens in November 1863. Jasper is invited to Box 7 where Mrs. Colliver identifies him as the grandson of the man who had murdered her husband and stolen the Great Ruby. Simon returns and hides aboard the Water Witch. He murders Tom Loveday. Clarissa reveals her identity to Jasper as the daughter of the man who had murdered Ezekiel and commits suicide on stage. Jasper is imprisoned on the Water Witch by Simon Colliver, who relates the deeds of Amos. With the Golden Clasp united, Simon leaves Jasper for dead and travels to Polkimbra. Jasper is revived by Mrs. Luttrill and follows Simon to Dead Man's Rock, arriving just before midnight on 24 December 1863. Colliver, with the treasure before him, mistakes Jasper for Ezekiel and throws the Great Ruby into the waves. He is later taken to Bodmin Asylum, to be partly cared for by his mother. Jasper, with the remainder of the treasure, buys Lantrig back and has Claire buried at Polkimbra.