For the VOC, a shipwreck was not so unusual; it happened regularly during its long history. What made this shipwreck special was the extraordinary drama that followed. The commander of the ship, Francisco Pelsaert, together with all the senior officers, a few crew members and some passengers, left the disaster site in search of water, leaving behind 268 people still alive on the wreck. The commanders' group soon aborted the search for water on the mainland and made their way to Batavia (now Jakarta). This journey took thirty-three days. After their arrival in Batavia, Pelsaert was sent back to rescue the survivors that were still on the wreck. He arrived at site two months after leaving Batavia, only to discover that a mutiny had taken place.
A group of mutineers, with Jeronimus Cornelisz as their leader, had murdered a total of 125 men, women and children. After a short battle the mutineers were captured. The worst offenders were executed on the island after a brief trial. The lesser offenders were taken back to Batavia to be tried. In Batavia most of them were executed, after already having been punished by flogging, keelhauling and being dropped from the yard arm.
Commander Pelsaert died in the following year, leaving behind his journal of the events. This journal, together with a book written some years after the incident, Ongeluckige voyagie van 't schip Batavia (The Unlucky Voyage of the Vessel Batavia), made it possible to rediscover the wreck. Journalist Hugh Edwards published an account of the shipwreck and its rediscovery by Dave Johnson, Max and Gerard Cramer and Greg Allen, under the name Island of Angry Ghosts: Murder, Mayhem and Mutiny.
In 1972 the Netherlands transferred all rights to Dutch shipwrecks on the Australian coasts to Australia. Various items, including human remains, which were excavated are now on display in a museum in Fremantle, Australia.
A replica of the Batavia was built in Lelystad (the Netherlands) between 1985 and 1995.
In 2002 historian Mike Dash's book, Batavia's Graveyard: The True Story of the Mad Heretic Who Led History's Bloodiest Mutiny told the whole story in more detail than ever before, making extensive use of Dutch archival sources to explore the early life of Cornelisz and a number of the Batavia's other passengers and crew.
The was also retold in the form of an acclaimed opera, simply titled Batavia, composed by Richard Mills and first performed by Opera Australia in 2001.