The reason: He cannot command and prepare his defense at the same time.
He may or may not be acquitted of charges at a "Court Martial" and might be able to salvage his career.
In any case, Clancy, he is relieved of command.
"The captain is always relieved of command as soon as possible."
Relieved of command temporarily isn't "canned" or "fired" or in any way "sunk". Clearly, folks in this thread are saying that he can be aquitted and live to sub again, as a captain. Others are saying he's going to lose his job.
Clancy's all I have for my submarine lore. But I don't need any book to recognize bs when I hear it.