On her last voyage, the ship ran into a heavy gale within hours after leaving San Francisco harbor and steaming north. Most of the passengers on board the Brother Jonathan became seasick and were confined to their rooms by the continuing storm of “frightful winds and stormy seas”. Early Sunday morning, the steamer anchored in Crescent City harbor on the first leg of its trip to Portland and Victoria, B.C. After leaving the safety of the bay that Sunday afternoon, the ship ran headfirst into more stormy conditions. The seas were so bad near the California-Oregon border that the captain ordered the ship turned around for the safety of Crescent City. Forty-five minutes later on that return and close to port, the ship struck the rock, tearing a large hole in its hull. Within five minutes, the captain realized the ship was going to sink and ordered the passengers and crew to abandon ship. Despite having enough lifeboats to hold all of the people on board, only three were able to be deployed. Acts of courage and desperation, fear and self-sacrifice, were numerous. The rough waves capsized the first one that was lowered and smashed the second against the vessel's sides. Only a single surfboat, holding eleven crew members, five women and three children managed to escape the wreck and make it safely to Crescent City.
Among the victims were Brigadier General George Wright, the Union Commander of the Department of the Pacific; Dr. Anson G. Henry, Surveyor General of the Washington Territory, who was also Abraham Lincoln’s physician and closest friend; James Nisbet, a well-known publisher, who wrote a love note and his will while awaiting his death; and Roseanna Keenan, a colorful San Francisco madam, who was traveling with seven “soiled doves”. As a result of this tragedy, new laws were written to increase passenger-ship safety, including the ability of lifeboats to be released from a sinking ship.