Looking at the facts, there is an obvious explanation; for some reason the Captain and crew panicked and took to the ships boat. This could have been due to a mistake in sounding the pump and thinking she was sinking, or bearing in mind the nature of the cargo, there may have been an small explosion or rumbling in the cargo. We do know that when the cargo was finally unloaded in Genoa nine barrels were found to be empty.
The records atate there was a lifeboat, lets say Briggs ordered his men to abandon ship and snatched up his navigational instruments. In great haste they all left. It may be significant that the main halyard, a stout rope 3 inches in circumference, was found later broken and hanging over the side.
This is detailed in the cross examination of Augustus Anderson in the Admiralty inquiry where he states "there were ropes hanging over the side". If they were trailing behind the ship, waiting to see if she exploded, perhaps suddenly, the wind took off snapped the rope, maybe sinking the small boat at the same time. Even if it did not, it would have been difficult to keep afloat in a small boat in bad weather.
The records of the Servico Metrologico in the Azores says that the weather deteriorated that morning and a storm blew up involving gale force winds and torrential rain. The Captain of the "Dei Gratia" says in his sworn record that the weather had been blowing very hard for seven or eight days previous and had only moderated in the morning of the 4th.
So that left the poor people from the 'Mary Celeste' crowded into a tiny boat at the mercy of the Atlantic, in heavy seas. Perhaps the same violent rains quietened down the cargo and the final story is that Captain Briggs got it wrong and paid the ultimate price along with his wife, child and crew.
Another theory was that there was a mutiny, however, this was a very short voyage, with a small crew, a fair and experienced Captain and first officer. It seems unlikely that this was the cause.
The poor "Mary Celeste" did not enjoy a good fate either, she became regarded as a ship seamen, and owners, wished to avoid. She changed hands frequently. Twelve years later she sailed from Boston with a mixed cargo and was wrecked off the coast of Haiti apparently by her subsequent owners to cash in on her insurance.
But her history is probably typical of ships of the era. She started life as the "Amazon" and arrived practically a wreck in New York in 1868. She was sold in a public auction for $10,000 and arrested in Boston. From Boston she sailed to New York and was re-fitted at a total cost of $11,500 before she sailed into her fate in the history books.
To put the whole thing in perspective, when the court in Gibraltar had settled this matter (they were more concerned in ownership of the Vessel and the cargo, rather than solving any mystery) their next case was the forgotten derelict Vessel "The Latin".
Neither was the "Mary Celeste" the only vessel found abandoned, in April 1849 the Dutch Schooner 'Hermania' was found dismasted but otherwise sound, with the Captain, his wife, child and crew missing, and in February 1855 the 'Marathon' was found in perfect order abandoned.