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Kirk and Commodore Stocker

But why didn't command fall to the next person in the ship's regular chain of command, which I assume would either be Uhura or Sulu, both of whom were unaffected by the ailment?

Yes! This is an aspect of the episode over which it is very hard to suspend disbelief. With Trek's well-known naval foundations in mind, it has long been known that operating a vessel at sea, even in peacetime, is too hazardous to be entrusted to someone without considerable nautical experience. While army commands were still being handed out to aristocrats with little actual know-how, a warship commander had to have started learning the ropes–literally–in his teens. There were plenty of "political generals" in the American Civil War, but there were no political admirals.

The episode asks us to believe that Starfleet’s policy is that unqualified officers can take command of starships, and then goes on to vividly demonstrate why that's such a stupid policy.

Stocker is a staff officer, with no line experience. Kirk is a line officer. There are staff officers with line officer experience, but Stocker acknowledges he isn't one of them. Line officers can command a vessel, staff officers without line experience command a desk, or provide technical expertise.

These terms can be confusing. A “staff officer” broadly can be any type of officer in an assignment where they are working on a senior officer's staff, rather than commanding an operating unit or part of one. It's a job that one rotates through.

In the U.S. Navy there are two kinds of non-line officers: Staff corps officers, who are part of an established corps within the navy: supply, medical, chaplain, civil engineer, JAG. But there are also restricted line offers in fields like engineering, intelligence, cryptography, public affairs, music and so on. They wear the insignia of line officers, but obviously a bandleader could never be in line to command a warship.
 
The Stocker subplot is a little strained when we've seen Sulu commanding the ship (out of universe, before the producers realized what they had in Jimmy Doohan). Sulu even did so during the apparent outbreak of full-on war with the Klingons. Also, it seems as though Sulu (not to mention Spock, who was still in command of his faculties) had the authority and even the obligation to relieve Stocker when he ordered the ship into the NZ.

Regardless, the developments ratchet up the stakes and work.
 
So everything said here being true, why did regulations permit Stocker to assume command? Obviously Kirk, Spock, and Scotty were all incapacitated. But why didn't command fall to the next person in the ship's regular chain of command, which I assume would either be Uhura or Sulu, both of whom were unaffected by the ailment?
So the episode could happen. ;)
 
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