When Dr. McCoy grumbles once too often about the way the USS Enterprise ought to be run, Captain Kirk puts him in command of the ship before beaming down for what is supposed to be a routine diplomatic mission. Then Kirk disappears, and McCoy (forbidden by regulations to relinquish command) is stuck in the hot seat overseeing a rapidly deteriorating situation that quickly acquires unexpected Klingons and goes downhill from there.
This novel contains examples of:
- Badass Boast: McCoy all but turns these into a language of their own in this book, as he never speaks to a Klingon in anything but one the whole time he is in command.If you use that tone with me again, my boy, I'll open your ship up like a sardine tin, and later on I'll fish your corpse out of space and thaw it out and stitch it back together the old-fashioned way, with a needle and thread, and then I'll use your guts for garters.
[later]
Think again, Commander. This is Enterprise. She is more than one man, though that one man may have made her famous—or among you, infamous. She is four hundred thirty-eight people—to whom you're an interesting enough problem, but one that we're long used to solving. - Birthday Hater: As is common with him, Kirk gets angsty after another birthday, feeling lonely and even his earth friends are joking when is he going to settle down.
- Bizarre Alien Biology: While arsenic is a deadly poison to humans, it's revealed that for Klingons it's a necessary part of their diets and arsenic deficiencies can lead to physical and mental health problems for Klingons.
- Call-Forward: Starfleet is cracking down on captains going down with landing parties, as it will be in Picard's day.
- Character Development: Kirk refuses to take the "aggressive colonizer" approach to trying to get the ;At, having learned better.
- Embarrassing Nickname: The planet's official listing in Federation star charts is "1212 Muscae IV". Most of the crew, somewhat to Spock's puzzlement, refer to it as "Flyspeck".
- Klingon Promotion: Invoked by McCoy when the Klingons want to know where Kirk is. Not wanting to explain the situation to an enemy, McCoy instead claims to have killed him in a duel and taken command. Kirk is later informed of his own 'demise' by the very baffled Klingon captain.
- Language Equals Thought: It's mentioned that the Orion pirates' word for "stealing" translates into English as "getting paid".
- Lost in Transmission: McCoy is initially relieved when the Klingons start jamming subspace communications and interrupt a tongue-lashing he's getting from Starfleet Command, until Spock points out that, based on what the admiral was saying, he was just about to relieve McCoy of command—and since the order was never actually received, Spock can't carry it out.
- The Master: Inverted with the Master of the ;At, who is a stand-up guy and pretty charming... except for the ensuing complications thanks to his virtually kidnapping Kirk.
- Plant Aliens: The Lahit are basically walking fir trees. Upon seeing a group of them, McCoy snarks that Birnham Wood finally gets to come to Dunsinane.
- Punctuation Shaker: Lampshaded. The first Federation survey team sent to a certain planet reported that one of the three sentient species there was called the ;At, but forgot to explain how the semicolon should be pronounced. At the beginning of the book, the Enterprise crew generally pronounce it as a click; later on, Uhura says that it's probably more of a glottal stop.
- Tempting Fate: Kirk justifies leaving McCoy in command because: (a) it's funny; and (b) a captain has considerable leeway on assigning command as long as the situation doesn't seem too complicated. He really should have known better...
- Time Zones Do Not Exist: Averted. Temporary CO McCoy is woken up in the middle of the night due to a communication coming in from Starfleet that has to be responded to upon receipt.
- Translator Microbes: One of the subplots revolves around Enterprise's linguistics analysts working with Flyspeck's three sapient species to get their languages to work with the universal translator, and the struggles they run into. At one point, Kirk finds a very frazzled-looking crewmember working with the third species, who are basically slimes, who tells him "I need more adverbs."
- Worthy Opponent: At the end of the book, the Klingon captain says that if all ship's doctors are like McCoy, then he should seriously consider having his own medical officer killed. McCoy replies that, based on his own diagnosis of the Klingon captain's medical condition, he should have his doctor killed anyway—either his doctor is so incompetent that he isn't able to diagnose the captain's clear signs of illness, or his doctor has diagnosed it and is already trying to kill him by providing substandard care. Knowing Klingons, the second possibility is more likely.
- You Are in Command Now: McCoy is given the conn during a First Contact mission as part of a joke by Kirk. Then Kirk disappears into a temporal anomaly, a Klingon warship shows up, and Starfleet regulations won't allow McCoy to hand over command to any line officer until relieved by Kirk or Federation brass. He's not happy. Hilarity and awesome ensue.
- Discussed at length when Kirk decides to put McCoy in command. Kirk points out that while it is true that there is a chain of command, as Captain he has wide latitude to decide who to give the conn to in situations where there isn't likely to be any trouble.
