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The ship Challenger will always be remembered as the vessel that carried Wyville-Thomson and his team into oceanographic history. But the fate of the ship herself is not in keeping with the remarkable part she played in advancing the study of ocean science. Returned to the navy after the Challenger expedition, she went into service for the Coast Guard and served as a drill ship for the Naval Reserves.

She was decommissioned in 1878 and put on reserve. In 1883 she became a receiving hulk (a sort of floating warehouse) and remained as such docked in the River Medway. In 1921 she was demolished for scrap. HMS Challenger's figurehead is virtually all that remains of the ship. The figurehead is kept at the Southampton Oceanography Centre.