Firing the CO is one thing. For all 3 to go there is much more to this.
In the Navy, it's not at all unusual. Usually has to do with bad command environment, too many DUIs, drug issues, sexual assaults, or something of a command-wide nature.
In this case, and without knowing any facts other than presented here, I'd guess the XO screwed up and the CO and CMC tried to sweep it under the rug only to have someone lower in the command leak it out to higher-ups.