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Multiple realities
(covers information from several alternate timelines)
"And enough with the metaphors, all right? That's an order."
James T. Kirk to Leonard McCoy, 2259 (Star Trek Into Darkness)

A metaphor is a specific term, phrase, or often idiom, that is used to make a comparison between two common things that are not alike. These types of comparisons are often tools used to create an analogy.

Some species had languages that were heavily dependent on, or even based on, metaphors to provide clear communication within the species, such as the use of story-based metaphors in the Tamarian language (TNG: "Darmok") and the use of culinary-based metaphors in the Klowahkan language (LD: "A Farewell To Farms"). The universal translator tended to initially translate these metaphors improperly, which could impede communications with outsiders by obfuscating what the speaker was trying to say to varying degrees. When the universal translator was translating their speech literally, a Klowahkan could be generally understood but come across as overtly and annoyingly obsessed with food and give strange advice like cooking paella as an outlet for rage, while a Tamarian would be unintelligible to anyone not familiar with their culture's mythology. (TNG: "Darmok", LD: "Crisis Point")

Discussing the interruption in the USS Enterprise sensors caused by the red bursts detected in 2257, Commander Michael Burnham described the interruption as "like a compass at the north pole." Evan Connolly indicated he found the "metaphor" simplistic, though Burnham corrected him that her statement was more accurately described as a simile. Captain Christopher Pike admired her correction, noting: "He said you were smart." (DIS: "Brother")

In 2258 of the alternate reality, after hearing Leonard McCoy compare Hikaru Sulu's assignment in the captain's chair to a poker game, James T. Kirk responded, "And enough with the metaphors, all right? That's an order." (Star Trek Into Darkness)

According to McCoy actor Karl Urban, the line was inspired by his observation: when I read the script, I did say to J.J. that every line seemed to be a metaphor, and maybe we should cut some of these down, so he turned around to Chris [Pine] said, "hey, why don't you tell him to give it a rest with the metaphors?" [1]

William T. Riker referred to the Earth nursery rhyme, "What Are Little Boys Made Of?", which stated: "Girls are made from sugar and spice, boys are made from snips and snails... and puppy dog tails," to describe the "old-fashioned way of looking at the sexes" to the androgynous Soren. He later clarified that "physically, men are bigger, stronger" and that they "have different sexual organs." He also noted that "men can't bear young." (TNG: "The Outcast")

Upon his retirement from being the Grand Nagus, Zek appointed Rom to be his successor, explaining the role metaphorically as "It's a great responsibility to stand at the bow of the Ferengi ship of state. A Nagus has to navigate the waters of the Great Material Continuum, avoid the shoals of bankruptcy and seek the strong winds of prosperity." (DS9: "The Dogs of War")

Metaphors

"A mother hen"
"A princess in a very high tower."
This might be a metaphor referring to the Earth fairy tale Rapunzel.
"A stack of books with legs"
"A stitch in time saves nine"
"A trail of breadcrumbs" / "(A) trail of energy crumbs"
"A trail of broken hearts"
"A walking calculator"
"A walking database"
"A walking medical encyclopedia"
"A walking powder keg"
"A walking tin can with circuits for intestines"
"A walking pile of circuitry and memory cells"
"Achilles' heel"

Any single and potentially devastating vulnerability in an otherwise invincible enemy.

In the novelization of What You Leave Behind, Commander Kira Nerys calls the cargo bay doors of Dominion Headquarters the Dominion's "Achilles hell." Although she is corrected by Elim Garak, she is sure her pronunciation is correct.
"(Someone is) all thumbs"
"(A) battle of wits"
"Battle of the sexes"
"Beat the hell out of (someone)" / "Kick the hell out of (someone)"
"Beat the tar out of (someone)"
"Break (someones) heart" (TOS
"Who Mourns for Adonais?"; TNG: "The Last Outpost");

"Broke(n) (someones) heart" (TNG: "Haven", "The Hunted", "Brothers"; DS9: "The Muse", "A Simple Investigation", "Ferengi Love Songs"; VOY: "The Q and the Grey", "The Disease", "Fair Haven", "Inside Man")

"(a) breeze"

A task that is very easy to do.

"(to) breeze in"

Quickly enter a room with ease and confidence.

"Cabin fever"
"(The) cat's out of the bag"
"Character assassination"
"Chicken and the egg"

The "chicken and the egg" was a paradox, usually posed as the question, "Which came first, the chicken or the egg?"

"Cold feet"
"Friendly vessel"
"I burn [...]. My eyes are flame. My heart is flame."
"I dream of a galaxy where your eyes are stars and the universe worships the night."
"If you're going to ride in the Kentucky Derby, you don't leave your prized stallion in the stable."

"In a nutshell" (VOY: "Unforgettable", "One", "Drone")

"Life is an endless stream of choices"
"Life is but a dream"
"Moral compass"
"(The) mouth of that chasm."
"(The) mouth of the cave."
"(The) mouth of the wormhole."
"Music to my ears"
"My ears are better than the average dog's."
"My eyes are as mysterious as the stars."
"My love is a fever, longing still for that which longer nurseth the disease."
"My mind is floating between two places.
"Nerves of steel"
"Never judge a fruit by its skin"
"(Eating out of) / (in the) palm of her hand(s)."
"Put out to pasture."
"Saber rattling" (VOY
"Body and Soul"; "Rattle his saber" (DS9: "Broken Link")
"(A) savage thrust into the very heart of the Dominion."
"Shell of a man"
"Shell of flesh"
"Snake oil salesman"
"Smoking gun"
"The smell of hatred, the stench of jealousy permeates you."
"Time is the fire in which we burn"
"Time is running out"
"What burns in their eyes, fires my soul."
"Ying and yang"
The actual references are to "yin" and "yang."
"You are my anchor"
"You are my eyes and my ears"
"Your hair is looking particularly silky tonight."

See also

External link