To be fair, the word "red" was not uttered. "Put all decks on the alert," was Kirk's order.
True enough, that is the specific dialog delivered;
And,
If you go back and
watch the episode, immediately after Kirk calls:
"Put all decks on alert!", we hear the loud alarm klaxon,
and see:
1. a held close-up on a
Big Red Light flashing incessantly in the hallway outside of the Transporter Room; as we Fade Out to Commercial.
Judge for yourself if
all the visual and audio information indicates ending the teaser on a
Red Alert; or not;
and, if not you're positive of what the alert status is, continue watching, as we:
returning from Commercial,
to see:
2. a
Big Red Light flashing incessantly in the hallway;
and then, exiting the Turbo-Lift,
we see:
3. a Big
Red Notice, showing on the overhead display panel of the Bridge Station closest to the Main View Screen, informing:
Condition Alert, on a completely
Red background;
and then, in another shot,
we see:
4. a
Big Red Light flashing incessantly on the Bridge, next to the Turbo-Lift doors;
and, after Kirk orders:
"Screen on.",
we see:
5. a
Big Red Light flashing incessantly on the Helmsman's side of Main View Screen.
Now, I don't want to
"color" your impression in drawing a conclusion, with regard to exactly what alert-status the ship is under when they end the teaser, break for Commercial, and return to open Act I, based on
all the viewer-information...
but...they sure aren't yellow.

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