After my initiation as a Chief Petty Officer in the Navy, the judge gave a speech that charged us with “first and foremost, look after your men.”  I assume that “frocked” Chiefs of today are equally charged to take care of those sailors assigned to perform duties under their supervision.
    Commanding officers rely on subordinate officers to carry out essential orders in their respective departments to “fight the ship.”  Those division officers rely on their respective Chief Petty Officers to function effectively in keeping their division manned and ready, by training and assigning sailors to perform expeditiously what they have been taught to do, to work as a team. 
    This is the “Chain of Command.”  Going “up the chain” means that sailors tell or ask the Chief what is needed, the Chief reports to the Division Officer, who goes to the Department Head, who goes to the Executive Officer, and he goes to the Commanding officer.
    Off the ship, the chain continues to Fleet Commanders, Staffs ashore, finally to the Secretary of the Navy.  His boss is the DoD and his boss is the President.
    So, what happens if the chain is broken by one of the links not responding effectively?  Does the problem go away, does the ship “take it in stride” or does the downward chain from the Commander to the “seaman deuce” suffer the consequence?  
    Can a Commander go “outside” the chain of command?  Yes, he can.  I’ve seen it done.  It happens in every department in the Navy.  It’s called “trade offs.”  For instance, between two ship’s supply departments, I’ll trade you coffee (which I have in abundance) for toilet paper (which is needed). 
See   http://submarinesailor.com/History/toiletpaper.asp

Having read Capt. Crozier’s letter in its entirety at: https://www.sfchronicle.com/bayarea/article/Exclusive-Captain-of-aircraft-carrier-with-15167883.php           (you have to scroll down the page to get to the actual letter.)  IMHO it says nothing out of the ordinary, he’s telling his superiors the facts and request space be set aside in Guam (their current location) because CDCs requirements for “social distancing” cannot be achieved on board the ship.
    His mistake, according to ‘national security’ was the way the letter was transmitted, i.e.,  over unsecured and unencrypted channels.  The contents were never challenged for being inaccurate, only the way it was handled and no one is concerned about the leak to the San Francisco chronicle.  When the sh*t hit the fan, bureaucrats in the Navy Department became unglued. 
    The Assistant Secretary of the Navy took the knee-jerk reaction to relieve Capt. Crozier.
For what?  Oh, yes, going outside the chain-of-command, which he clearly did NOT do, it was because the SF Chronicle published the letter, embarrassing the SecNav and SecDef.
    On April 5th, Capt. Crozier tests positive for the coronavirus.
    Asst SecNav Thomas B. Modly resigned.
    I’m waiting to see if the Commander-in-Chief restores Capt. Crozier to command.