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I was recently rewatching Star Trek: Deep Space Nine, and in particular, the episode Tears of the Prophets (Season 6, episode 26). A major plot point in this episode revolves around former Leader of Cardassia, Gul Dukat, attempting to find a way to bring in Dominion reinforcements through the wormhole. In particular, Dukat releases a Pah-Wraith from a small figurine and subsequently becomes possessed by it.

What is interesting, however, is that Benjamin Sisko receives a vision shortly before this from the atemporal prophets warning him that Bajor is in danger:

[Ops]

WORF: The Sisko is of Bajor.

[Wardroom]

MARTOK: It is where he belongs.

[Captain's office]

ROSS: It is where he is meant to be.

SISKO: Are you telling me not to go to Cardassia?

[Ops]

ROSS: The Sisko is of Bajor.

MARTOK: It is dangerous to walk a different path.

SISKO: Dangerous? In what way?

ROSS: The Sisko must not leave the chosen path.

WORF: The Sisko is of Bajor.

LETANT: It is where he belongs.

SISKO: Why is it dangerous to leave? And how will it affect Bajor? You have to tell me.

(The vision ends.)

This is routine for Sisko, being emissary of the prophets, but much more surprising is Admiral Ross's response to the vision:

SISKO: The Prophets don't see me as a Starfleet captain. They see me as their Emissary.

ROSS: That's the problem, isn't it? For the past six years you've tried to be both, and up to now I've been patient. I've indulged you, I've gone out on a limb for you many times, but this is it. You've got to make a decision. You are either the Emissary or a Starfleet captain. You can't be both.

In which Ross tells Sisko to deal with his conflict of interest. The problem with this statement is that not only is the Bajoran religion demonstrably, provably true, but the prophets are instead instrumental to the outcome of the war by preventing Dominion Reinforcements from coming through the wormhole!

In this case, the logical conclusion is that the 'Emissary' of the prophets is certainly an extremely valuable strategic tool for the Federation to hold, and one that they never use and actively refrain from encouraging.

Why does the Federation not attempt to use the prophets to their advantage? Is it because Bajor is not a Federation planet and has a non-aggression pact with the Dominion or due to some ramification of the prime directive?

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    Poking god-like aliens is a terrible idea. Why didn't they ask Q to snap the Dominion out of existence? Why didn't they contact the Organians and ask them to make the Borg go away? – Valorum Jun 14 '20 at 13:42
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    +1. I had a similar thought when I re-watched DS9 recently. They treat the Bajoran religion as if it was “hokey religion” when it is actually the real thing. – Darren Jun 14 '20 at 14:46
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    @Valorum The difference is that the Prophets have already helped them in the past (in a particularly monumental way) and their prophecies have directly affected the Federation before, in which case ignoring their heed is asking for trouble. One would expect the Federation to take a look into what exactly made 2700 Dominion ships vanish (at the minimum). – Lt. Commander. Data Jun 14 '20 at 15:09
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    @Darren They treat the religion as "hokey" because they view the religious elements of it as hokey. They believe that there are wormhole aliens, and that they are non-temporal, or super-temporal, or whatever they may be. But they view the Bajorans' attitude toward the wormhole aliens as primitive--they are not "Prophets," they are just aliens who contacted the Bajorans in the past. – Yehuda Jun 15 '20 at 16:33
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    Hokey religions and ancient weapons are no match for a good blaster at your side, kid. – Jack B Nimble Jun 17 '20 at 4:33
4
+50

The Prophets don't care about the Federation. They warn Sisko of threats to Bajor. In his role as "The Emissary", Sisko is (in effect) acting as an Ambassador between two non-Federation races.

Admiral Ross' objections might reduce considerably if Bajor joined the Federation, but Starfleet's Ambassadors are still shown as separate from their Captains.

Plus, outside of Sisko, the Federation don't seem have anyone with whom the Prophets would be particularly willing to communicate. And, from Season 3's "Prophet Motive", they have an incentive not to try and force the issue.

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In this case, the logical conclusion is that the 'Emissary' of the prophets is certainly an extremely valuable strategic tool for the Federation to hold, and one that they never use and actively refrain from encouraging.

This is not technically true. In "Sacrifice of Angels" (episode 6x06, DS9), Sisko convinces the Prophets to destroy a large fleet of Jem'Hadar ships. The Prophets are initially reluctant to intervene, and seemingly uninterested in the Federation's needs (note: all characters other than SISKO are actually the Prophets appearing in various forms):

[Captain's office]

DUKAT: You desire to end the game.
SISKO: What game? I don't understand.

[Wardroom]

WEYOUN: You seek to shed your corporeal existence.

[Bridge]

DAMAR: That cannot be allowed.

[Promenade]

ODO: The game must not end.
SISKO: The game? You mean my life? Is that what this is about? You don't want me to die?

[Captain's office]

DUKAT: The game must continue.

[Wardroom]

WEYOUN: You are the Sisko.
SISKO: Believe me, I don't want to die, but I have to do everything I can to prevent the Dominion from conquering the Alpha Quadrant. If that means sacrificing my life and the life of my crew, so be it.

[Quark's]

JAKE: We do not agree.

[snip]

KIRA: We have every right.
SISKO: Fine. You want to interfere, then interfere. Do something about those Dominion reinforcements.
ODO: That is a corporeal matter.
DUKAT: Corporeal matters do not concern us.
SISKO: The hell they don't. What about Bajor? You can't tell me Bajor doesn't concern you. You've sent the Bajorans orbs and Emissaries. You've even encouraged them to create an entire religion around you. You even told me once that you were of Bajor. So don't you tell me you're not concerned with corporeal matters. I don't want to see Bajor destroyed. Neither do you. But we all know that's exactly what's going to happen if the Dominion takes over the Alpha Quadrant. You say you don't want me to sacrifice my life? Well, fine, neither do I. You want to be gods, then be gods. I need a miracle. Bajor needs a miracle. Stop those ships.
WEYOUN: We are of Bajor.
DAMAR: But what of the Sisko?
ODO: He is intrusive.
DUKAT: He tries to control the game.
JAKE: A penance must be exacted.
WEYOUN: It is agreed.
DUKAT: The Sisko is of Bajor, but he will find no rest there.
KIRA: (touches Sisko's left ear) His pagh will follow another path.
SISKO: What path is that?
[no answer is given, but the Prophets do as Sisko asks.]

(Transcript courtesy of Chakoteya.)

From this exchange, I think it's fairly obvious that the Prophets have no interest in "negotiating" with anyone. They are playing their own "game" which only tangentially involves the Federation, and only to the extent that the Federation is a friend of Bajor. Even within those constraints, they seem to want Sisko et al. to solve their own problems, without the involvement of the Prophets. The only apparent exception is to directly oppose the Pah-wraiths, as in "The Reckoning" (6x21, DS9), where a Prophet and a Pah-wraith each possess a humanoid and have a duel on the Promenade. The Dominion, and other "corporal" concerns, are simply not of interest to the Prophets, and the Federation has little of value to offer them. So any negotiation would be fruitless.

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They already did. It's hard to maintain a dialogue with a species that has no comprehension of linear time. And Starfleet already did that when Sisko and Dax discovered the Wormhole

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