Navy Capt. John Banigan is no longer aboard the San Diego-based guided missile cruiser Lake Erie.
Neither is a goat named Master Chief Charlie.
Banigan was ousted from command this week after the brass lost confidence in his ability to lead, the standard explanation when a commanding officer is removed.
Banigan has been reassigned to a desk job. Master Chief Charlie is also ashore, though it remains unclear whether he is on Navy property or civilian property. He is, however, in excellent health, the Navy said.
The fate of the captain and the goat became mixed when the Navy began an investigation into the command climate aboard the Lake Erie, which was reassigned to San Diego from Hawaii in September.
According to Navy Times, one of the things that investigators found was that Banigan allowed Master Chief Charlie to make the trip from Hawaii to San Diego.
Banigan may have failed to comply with the rules of the California Department of Food and Agriculture that require anyone bringing farm animals into the state to have them checked out by a veterinarian.
The exact reason for Banigan's removal as the ship's skipper remains unclear. The Navy declines to comment.
Master Chief Charlie's unofficial role as the ship's mascot was no surprise.
He had appeared at numerous events in Hawaii, often bleating at interesting moments to the delight of crew and family members. He was pictured with sailors and with the Navy's top admiral.
There is a long history of the Navy and goats. Nothing prohibits goats -- or other livestock -- from coming aboard ships, although there are rules to be followed.
The area where senior enlisted sailors sleep, lounge and eat aboard ship is called the goat locker. The mascot of the Naval Academy is a goat. In the early days of the Navy, goats provided a source of fresh meat when ships were at sea.
The U.S. Naval Institute last year published "A Brief Illustrated History of the Navy Goat." With their sure-footedness, swimming ability, compact size, and willingness to eat anything, goats were better suited to sea voyages than, say, cows, the history noted:
"A half-ton cow being tossed in a storm could be as dangerous as a loose cannon."