Alas, we did see the topside of the ship's aft hull clearly enough to observe that when the Defiant flies between the nacelles, a beam fires from the big hump at the pylon stems, and then ceases firing, revealing a smooth surface devoid of emitters... Hmm. Perhaps the clever TOS rapidly-extendable-and-retractable-emitter (or cloaked-emitter?) technology hasn't been entirely forgotten.

Probably the lack of visible weapons on the TOS ship would best be explained by saying that the emitters were covered by hatches or "gunports". These ports would be an anachronism from the time when shields were primitive and starship hulls were coated with physical armor (a possible Romulan war era practice - remember the physical-armor "shields" of the Neutral Zone outpost in "Balance of Terror"?). For any ship built after the 2240s, these gunports would be omitted since they would no longer serve any practical purpose.

Then we could have the TOS ship, *and* the myriads of TOS-era fanfic designs with FJ-style visible, paired emitters. Those fanfic ships (at least the versions seen, if not their original pre-TOS prototypes) would simply date from after the 2240s. Or whatever date one chooses for the abandoning of gunports. Big and fancy ships like Constitutions might retain this feature longer than others, for decorative purposes.

Something rarely mentioned-or considered-is that the phaser banks actually were coupled. Via the lit up dome on the bottom of the saucer. In theory, the dome phaser's might function as a predecessor to the phaser array strips of TNG.

Of course a lit dome is also atop the bridge, which would give a clear, aft firing arc. I know, I know. The bridge is there... Who knows how the actually emitter's are fed power? Otherwise, I see nothing wrong with the concept. At least where the bridge is concerned, we don't need a Phaser Control Room.

Beyond "what we see" in TOS, nothing really substantiates or eliminates this possibility. The technology is so vaguely defined for TOS anyway.

More modern, TOS movie starships clearly redefine the approach to weapon arrangement. Not to mention the domes having been redefined as part of the Navigational Sensor System. For the sake of discussion, it is possible that the leaps in technology could be that dfferent by TMP.

Also, where is it stated that the dome in the TMP ship was a navigational sensor array specifically? Granted, this makes sense, but the thing could also be a planetary survey sensor array (since it doesn't enjoy a very good view forward) or even an auxiliary nav deflector system (or a primary one for those ships that lack the big blue dishes, like Miranda or Constellation).

Again, where is it documented that the main phaser arrays on the bottom of the saucer are coupled through the lower dome? It's an interesting idea, yes, but I would like to know your source.

The majority of noncanon sources list the domes on the priamry hull of the TMP Enterprise as the "upper and lower navigational domes/sensor arrays." I have a feeling they are NOT deflectors. How would they operate? Timo, you yourself say they do not have a very good view forward, so if they aren't good as sensor arrays, they'll be less effective as deflectors.
And those lighted things the domes sit on on the TMP ship are just that, lights. Not anything else. In case people didn't know.

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In conclusion, there is NO WINDOW on the bridge module of the original E. And as I said before, there isn't enough room under the dome for it to be a completely transparent walled second deck. That doesn't even make any sense.

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Timo/Daniel:

Thank you for your comments.

According to the TMP blueprint's, designed by Andrew Probert, the dome's both below and atop the bridge, function as a 'navigational dome'. I assume they are components of the Warp Celestial Guidance system also referred to in the same blueprints.

Regarding the domes function as part of the TOS design? Unless my misplaced copy of "The Making of Star Trek" (Roddenberry's writer's guide is part of that book) does say, there is nothing written (i.e. a source) that establishes their function. I merely suggest that since the lower dome is "lit", and we do see the weapons discharge from that area, that there may (or may not) be a connection of some kind. If I am correct, than I further suggest that multiple emitter's (or turrets) are mounted within the dome. It would account for primary and secondary phaser banks that have been mentioned above.
The upper dome is also "lit" and therefore might (or might not) be a component of some kind that is mounted upon the roof of the bridge module.

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"...screw logic, let's go for a theory with no evidence!" - Omega.

Irony ensues.