Star Trek: Deep Space Nine/Headscratchers

The terrorist is right?

 * Kira's reaction when confronted with her crimes in "The Darkness And The Light". She killed innocent people. She admits it, and she doesn't feel the least bit guilty. Her response is to get angry at the guy who tells her how many innocents she hurt and yell at him that he was a legitimate target because he was a Cardassian on Bajor and it didn't matter whether he was a member of the military or not. And that all of the other people she killed, whether adults or elderly or children, whether military or civilian, whether armed or unarmed...they all deserved it because they were Cardassians on Bajor. After seeing that episode, I was glad that one of her victims put her through hell by murdering the other members of her resistance cell. She deserved it, and so did they.
 * Your mileage may vary, but I love this episode for being one of the few episodes to show that several issues are multi-sided. One man's terrorist is another man's freedom fighter.
 * Kind of ignoring the circumstances of the statement. Kira was not only in the last stages of pregnancy, so the extra hormones weren't helping, the man was planning to cut the baby out of her, a baby that wasn't even hers but actually her close friend's, after she spent days watching her friends be murdered one after another. Had he merely shown up at the station and asked for an apology she may very well have given it to him, she had an entire episode in the first season where she learned the valuable lesson that not all Cardassians were monsters and should be punished solely for existing. Neither of them were particularly rational about the subject by that point.
 * Kira was shown to be a fanatic, and a self confessed terrorist. Try finding an example of such a character in a heroic light post 9/11.
 * Yeah, because there weren't major acts of terrorism that caused the deaths of many people before that, right?
 * That doesn't change the fact that the 9/11 attacks left a major impact on American society and definitely killed any chance of showing unrepentant ex-terrorists in a good light.
 * Only if those terrorists aren't on America's side, or that of an America-like society.
 * I personally thought it was great that she wasn't apologetic. She didn't try the "you're right, we all did things we had to do, it was war, can't we all get along?" card. She went right out and said, "Whether you were a military general or you picked up garbage for a living, you were a legitimate target!" Try to put yourself in her shoes... your country has been successfully invaded by a brutal dictatorship that enslaves, rapes and murders your people. I'd say the same damn thing.
 * The main problem with the episode was it completely contradicted the much better season 1 episode "Duet", where Kira managed to mature past that black and white worldview and accept that the people at the bottom weren't automatically guilty. Darkness and Light was a real step backwards in both Kira's character development, and the maturity of the show as a whole.
 * One way of reconciling "Duet" and this episode is that in "Duet", Kira was forced to accept that Cardassians weren't all monsters, and some were truly good people. Note that Kira never disagrees with Marritza's claim that all Cardassia is guilty of the crimes during the Occupation. But in "The Darkness and the Light", Kira was dealing with an insane murderer. Her musings at the end made me think that she pitied Prin on some level, but that she felt she wasn't wrong.
 * Provoking these kinds of questions was the episode's point. I'm not convinced it does it especially well, but credit where credit is due.
 * It's debatable if those people were truly innocent. They were taking advantage of oppression, enslavement, and murder to live their lives as they wished.
 * Were they? The Cardassian Union seems to be highly autocratic. They might well have been conscripted into their positions. When you live in a dystopian dictatorship where dissent is punished with death, sometimes "just following orders" is a legitimate defense.
 * It's hard to say how legal theory might work several centuries from now but the defense of simply following orders hasn't protected anyone from being arrested for simply being guards at Nazi concentration camps.
 * Nazi concentration camp guards weren't forced into those jobs against their will. They would've either volunteered or been specially chosen for their obscene loyalty to the Nazi party and/or hatred of Jews. And we're not talking about a guard at a Cardassian death camp here. We're talking about a household servant. He probably had no choice at all in where he worked or who he worked for.
 * Actually, some Nazi concentration camp guards were in fact forced into those jobs against their will. The Nazis had a lot of camps to run and not always enough men to staff them. They were already forcibly conscripting soldiers for front-lines fighting, they did the same for some of their camp guards, essentially telling them "Do what we say or one of the loyal German guards will shoot you first and then do whatever we told you to do anyway." Being a concentration camp guard was not some elite position given only to the most loyal and Jew-hating, it was just military duty, and like they felt free to use conscripted/slave labor for everything else, Nazis used conscripted/slave labor for that as well.
 * Incorrect. Anybody who was a concentration camp guard was ultimately there because they chose to be. German military regulations of the period allowed anyone to request transfer from any assignment for the purpose of assuming duties closer to the fighting front. So even if they were conscripted, concentration camp guards would only stay there in lieu of regular military duty (such as going off to fight the Allies) if they made a conscious decision of their own that they'd rather stay back where it was safer, even if it meant having to throw Jews in gas ovens. And once you've made that decision to voluntarily continue participating even if you have an 'out', you are morally liable for what happens.
 * I'm sure forcible conscripts were allowed the full privileges of German military regulations.
 * First off, the death camps were administered by the SS, which didn't use conscription until 1944, so the entire point of 'forcible conscripts' is moot -- until the very end of the war, the SS didn't use conscripts.. Second off, large amounts of personnel were being transferred from concentration camp guard duty to combat posts on the Eastern front as early as 1941, so clearly they were indeed doing precisely this.

Medieval Bajoran Spacecraft

 * In Explorers Sisko builds an exact replica of an old Bajoran lightship; a starship that doesn't use engines but operates using solar sails. Exactly how technologically advanced where the Bajorans at the time the original model was built? (Note the gravity net was the only modification Sisko made.) The entire thing is operated soley by cranks and pulleys, there is not any sign of a computer or even much of a power source for that matter. So how exactly did the ancient Bajorans get the original lightship into orbit? Were they somehow able to build a rocket capable of breaking orbit yet somehow not have the technical knowledge to build powered motors for a pulley system?
 * An orbital tether/stratotower maybe? A technology that would be démodé once transporters became available - why spend hours riding a vertical cablecar once you get a tech that can bounce you thousands of miles in seconds? See the Voyager episode that featured this tech.
 * The Prophets did it.
 * It's never stated this is the only form of interplanetary travel ancient Bajor had access to. In fact, we really don't know all that much about Bajor's tech level before the Occupation, but they probably were not pre-warp at the time. Another episode featuring a lightship implied that although the tech was ancient, Bajorans were still using them 200-300 years before the series, even though they were obsolete by then, just like O'Brien likes to shoot the rapids in a primitive kayak when he could easily simulate a more modern, powered vehicle in the holosuites. As for the manual operation of the ship? Maybe they just liked it that way. They might have brought portable computers like laptops on board, too, but that's just speculation. My personal theory is the ancient Bajorans launched these things up in single-use disposable rockets, like the solid-fuel boosters on the space shuttle, that could get the ships into orbit but couldn't go much further. But I also think Bajor was warp-capable and probably had at least a few off-world colonies before the Cardassians invaded, as per Picard's comments in the episode that introduced them that the Bajorans were accomplished artists and architects when humans were still ice age hunter-gatherers.
 * Just had a thought. Perhaps the Bajorans did have access to electricity and motors and stuff but intentionally left it out of the design for some reason. For example, if the ship were to encounter an EMP wave that would cripple the ship. Maybe the Bajorans were expecting something like that to happen. They explicitly mention the Denorios Belt bring a major concern and that's a plasma field within the Bajor system. Surely that would have caused major problems for a ship that does have a power source, right?
 * If they were advanced enough to launch the ships then shouldn't they have been advanced enough to know the basics about protecting electronics? It would seem far more dangerous that without sensors and computers they would go far off course. Of course, unless the Cardassian home planet is in the same system as Bajor it makes even less sense that anyone would try it. Anything less than warp speeds couldn't make that long a trip safely (something an experienced officer like Sisko should know).
 * Maybe they launched the lightship and an orbiter in a rocket. The lightship undocks, goes flying around exploring, returns to orbiter and redocks, orbiter initiates landing.

But the Other Dax did it!

 * In a culture that regularly changes hosts, why don't the Trill have a precedent for crimes committed by a previous host?
 * They probably don't prosecute. One of Jadzia's previous hosts committed murder, they simply erased any record of him and repressed the memories within the symbiont. Odds are they just write any problems like that off as a problem with the host. Hell, Dax has two, possibly three, hosts (the murderer, the guy who stole it for a few hours and possibly the future one from that one planet) that commit serious crimes and nobody ever seems to think there may be a problem with Dax itself for allowing the actions to happen.
 * Trill society could easily have one. However, the symbionts have only been open knowledge to all races within the last couple of years, so it would have been dealt by Trill alone, and other species would not have precedent on the books yet. Tandro wanted Dax to be tried by Klaestrons, presumably so that Dax would be executed and he would have 'avenged' his father's death.
 * So when they got the Trill expert witness, why didn't they just ask him what their policy was for the crimes of past hosts? They never did.
 * No human government refrains from punishing simply because a criminal had a spouse and children. They have to suffer and in a sense they are punished collectively even though that is not the intent of the law. Trill probably made the same reasoning about symbionts.
 * Since the Trill system seems to go out of its way to erase any mention of a former host committing a crime and pretends that its system is perfect it's entirely possible that there isn't a single publicly known crime committed by a symbiont until Jadzia was put on trial (and acquitted). They may have decided in their arrogance that since no host would ever commit a crime there was no point in working out the legal ramifications.
 * Then where was the "why the hell are we talking about this? A joined host couldn't have committed the crime" speech from the Trill expert witness?
 * Out-of-universe probably because that point about Trill mentality wasn't established in season 1. In-universe because a government willing to kidnap a Starfleet officer and only after they were caught try to invoke an extradition treaty probably isn't going to listen to a Trill arguing that no host would ever commit a crime and the Bajoran arbitrator would be justifiably skeptical as well. Frankly that's not the strangest of the episode's problems since no one points out the weakness of the 'we confirmed every other suspect's location' evidence and Sisko argues only about the nature of Trill hosts without trying to look into the prosecution's claims.

Idiotic Federation Treaties

 * In another "Dax"-related question, who in the world does the Federation come up with to make these damn treaties?! Signing a treaty with the Romulans promising not to develop cloaking technology was bad enough (and yeah, I read Serpents Among the Ruins, and I get that It Makes Sense in Context). But signing a treaty with the Klaestrons allowing for unilateral extradition?! What Could Possibly Go Wrong?
 * Unilateral extradition isn't that odd by itself (at least, it's not an inherently ridiculous concept), but if the Federation is really based on the EU, they would never for a moment consider handing Dax to a government that used the death penalty, without the explicit assurance that the entire plot of the episode wouldn't happen.
 * The series itself never explains the full terms of the Treaty of Algeron, but presumably in return for not developing cloaking technology the Federation gained some concession from the Romulans.
 * The concession the Federation got was the Neutral Zone, which is meant to be a buffer that keeps the Romulans from cozying up to their border or spying on them. Of course, the Romulans violate it with impunity... but then we learned in TNG that the Federation futzes about with cloaking technology on occasion as well.

Cross-breedin' Cardies

 * How the heck does Dukat keep having half-breed children? If a Trill and a Klingon need medical interference to make a baby possible than shouldn't Bajoran/Cardassian offspring require even greater intervention? One is a mammal, the other a reptile!
 * It is never stated in canon that Cardassians are reptiles, though it is admittedly a sensible assumption (but then why do they have hair?). The troubles with species interbreeding has no beginning and end.
 * Reptile scales and hair are both made of keratin, so it isn't that unreasonable to hypothesize that Cardassian hair is just a modified set of scales (possibly evolved as some sort of sexual display characteristic). Dinosaurs had feathers too, which again is just a form of keratin.
 * For that matter, scaly mammals exist on Earth. Just take a close look at an armadillo's armor plating, or the tails of beavers and rats.
 * Word of God is that Cardassians have both reptilian and mammalian characteristics. It's also implied that Ancient Bajorans visited Cardassia in lightships before Cardassians were warp-capable, so modern Cardassians might already have some Bajoran heritage they just don't know about or won't admit.
 * In Worf and Jadzia's case, the problem may be related to the symbiont, or rather, exacerbated by it. We know that Dax's previous female hosts have been mothers, so it's entirely possible that a symbiont and a Trill fetus can coexist. Perhaps it's simply more difficult for a symbiont and a Klingon/Trill hybrid fetus to coexist, and requires medical intervention. Maybe the hybrid fetus stimulates the Trill mother's immune response to the point where it begins to attack the symbiont.
 * Good theory, especially in light of the physical location of the symbiont (very close to the womb in female Trill). There could be all sorts of autoimmune side-effects in that area of the female Trill's body that wouldn't take kindly to Klingon DNA, or any non-Trill DNA in fact, designed/evolved entirely to prevent disruption to the symbiont/host link.
 * This raises another question about the Trill: How does a symbiotic relationship between two species evolve when one of those species must be surgically implanted into the other?
 * Maybe the surgery is a more modern procedure that replaced a less sanitary, natural method of implantation?
 * Possibly symbionts originally lived out their entire lives in their first host, which they entered as eggs/larvae, and died when the host did. Surgery to transfer the symbionts was developed later, allowing symbionts' lifespans to exceed that of their hosts for the first time.
 * Bajorans and Cardassians, despite appearances, are more closely-related than Klingons and Trill, I guess. They do live within, like, a parsec of each other, if I recall correctly.
 * And the solar-sailer episode suggested that there's been interaction between Bajorans and Cardassians for millennia, as I recall. That's a lot longer than humans and Vulcans have been in contact. Maybe they've done some genetic retooling over the years or something along those lines. The Cardassians have certainly been known to do it within the canon of the series itself, albeit for rather more politically-motivated purposes.
 * Some EU stuff, especially A Stitch In Time, states that the Cardassians have basically been conquering other races and taking their planets for pretty much their entire recorded history. (Probably having decided to deliberately ditch any history before that.) While in the modern day they have some (very lightly-adhered-to obviously) regulations against interbreeding, it probably wasn't always that way. Indeed, A Stitch In Time heavily implies that the modern version of the Cardassians we see is the result of them interbreeding with the native inhabitants of the planet now called Cardassia Prime to the extent that the natives were effectively assimilated completely into the Cardassian genepool. So probably Cardassians are a bit like humans in that their genetics are very compatible with other alien species.

We're more justified than you!

 * The Bajorans. While you can sympathise with their plight that they've had 50 years of Holocaust-style oppression under the Cardassians, it starts to lose its impact when they excuse themselves at every opportunity of doing some evil act as being what they would have done during the Occupation. Sometimes they actually seem more cruel and extremist than the Cardassians, which is ridiculous when they are supposed to be BETTER than that!
 * It becomes more egregious when you realise they had invented advanced technology BEFORE humanity even moved out of caves, what apart from religious fanaticism exactly stagnated the Bajorans so?
 * It's hardly uncommon in Real Life. A person or a group of people feel (and might be entirely correct in doing so) that they have been victimized and so any action they take is justified while any action against them is not . In the eyes of many Bajorans what happened was either entirely justified or forced to happen by the Cardassians.
 * In the Star Trek Terok Nor prequel novels, the reason for Bajor's "stagnation" is made clear: They have everything they need. Prior to the Cardassians' arrival, they had little interest in meeting with other races or even colonizing outside their star system, and those that did were considered fringe, at best.
 * A good comparison for this can be made with the Vulcans. They were way more advanced than humans, even leaving out Enterprise continuity. In the span of a few centuries Starfleet has outstripped them completely. The Bajorans just didn't have that drive.
 * At the start of the series, they've been out from under Cardassian oppression for something like a year. The Cardassians have just barely left the planet. It's not like the occupation is a generation or two in the past like the Holocaust is for us, it is something that just happened. It really shouldn't be that hard to understand that they're still coming to grips with what happened to them and that they're quite likely to remind everyone of just why they're in the position they're in.
 * Just rewatched recently. It wasn't even a year. The Cardassians had only even left the space station at most two weeks ago.

Who's responsible for the Maquis?
"Sisko: You can't do an illegal search on a Federation citizen. Odo: She ceased to be a Federation citizen when she helped the Maquis."
 * SF Debris brought up an interesting headscratcher regarding the Maquis. There are two possible scenarios:
 * 1. The Maquis (and by extension, the rest of the Demilitarized Zone residents who have been left high and dry on the wrong side of the border) are still Federation citizens. And yet they take actions against the Cardassians. This would create a war.
 * 2. The Maquis are no longer Federation citizens (as was implied by dialogue in the episode "Journey's End", specifically Picard's admonition "I want to make absolutely sure that you understand the implications of this agreement. By giving up your status as Federation citizens, any future request you or your people make to Starfleet will go unanswered. You will be on your own and under Cardassian jurisdiction.") And yet the Federation attempts to protect them, which would eventually create a war.
 * This is probably where it all went wrong. Picard managed a sensible compromise (or as sensible as was possible under the circumstances), keep your citizenship but leave, or stay but become Cardassian citizens. That is straight forward enough; clearly when it came to time for Federation Ambassadors to formalize that someone back-pedalled, took a clear-cut compromise and created a quagmire because it seemed "nicer".
 * There is suspicion that Kasidy sold medical supplies to the Maquis. Odo wants an illegal search to gather evidence.


 * Holy Patriot Act, Batman. Fed citizens have inalienable rights, but any policeman, even a foreign policeman can cancel your citizenship and rights on suspicion???
 * Odo also has a bit of a history of Orwellian beliefs so i'm not surprised he acts that way.
 * The Maquis have de facto renounced their Federation citizenship, basically saying "We are not going to recognize your laws, your authority, or your needs"... but still perfectly willing to get the Federation involved in things because of them, natch. They might not have signed papers specifically relinquishing their Federation membership, but under common law they're likely stateless until they decide to surrender themselves to Federation authority. Odo could be saying that by helping the Maquis, Kasidy is Maquis, and thus declaring herself not a Federation citizen. Also, probably best not to take what Odo says too literally.

Will the real Darhe'el please stand up?

 * This is not to knock "Duet", which is one of the best episodes of the series and in all of Star Trek in my opinion. But one wonders exactly how Marritza expected his plan to work. If Darhe'el had been alive, all the Cardassians would have to do to discredit Marritza is simply produce him. And if he were dead, just tell everyone that-- hell, half of Cardassia viewed his body! So whether Darhe'el were alive or dead, there was no way Marritza would be able to convince people that he was him. This was not a very well-thought-out plan on his part.
 * He probably wasn't thinking that far into it, having lived with years of pent-up PTSD, guilt, and self-hatred driving him into his plan. Most likely he thought that with his Card-Carrying Villain persona, the Bajorans wouldn't bother to conduct a thorough investigation. Although if he had survived, it's probable that he would have been able to publicly explain his actions, which may still have gone some way to achieving his goal anyhow.
 * He might not have expected the crew of DS9 (or wherever he ended up captured at) to actually contact the Cardassians and check. This would be a fair assumption assuming the station were run solely by Bajorans, perhaps he didn't know about the Federation involvement (which happened only a few months before he arrived.)
 * Or having checked, he might expect them to believe that the Cardassians had lied. After all, it's not like the Cardassians were above lying to save face on, well, just about anything. If it hadn't been for them then they might well have assumed that the Cardassians were trying to create an alibi.
 * In fact, after receiving that information from Dukat, DS9's crew did assume that it was forged-- at least, Kira certainly did. It was the dermal regenerative Marritza was taking that tipped Bashir off.
 * As to the real Darhe'el not being alive, Marritza almost certainly knew that. He was connected to the man after all, probably some other living soldier from that camp that was now living on Cardassia contacted him when Darhe'el died to let him know. As to getting away with it without Cardassia debunking his identity: he didn't know that Garak was there to rat him out so quickly, and probably figured that the Bajorans would have him tried and executed practically before Cardassia even heard about it.

If you eat at my restaurant, you'll be making a mistake you'll regret for the rest of your lives!
"Joseph Sisko: Now I don't want to see anyone studying the dessert menu. If you order anything but the bread pudding souffle, you'll be making a mistake you'll regret for the rest of your lives."


 * Is that really how restaurant owners talk? Throwing a big chunk of their own product under the bus?
 * When a restauranteur constructs a cult of personality for themselves, as Daddy Sisko has, that's hardly implausible. Bear in mind, this is a guy who has no respect for his medical doctor because he doesn't know the difference between Cajun and Creole food. He's a cantankerous old man with some misplaced priorities, and should be thought about in this light.
 * Of course, since no one needs money in the Federation, what does he care?
 * It's not about money, but about professional pride.
 * Could have just as easily been the special for the night, and he was being hyperbolic when he said it.
 * Shit, maybe he'd just realised he'd forgotten to get the ingredients for anything except a bread pudding souffle (and how does that work, by the way?) and was extemporising to cover his ass.
 * If that's the case, then he certainly fooled Ben, who then says "you should listen to him. The man knows his bread pudding."
 * It's a turn of phrase. Don't be so literal.

Wartime extradition
"Sisko: What are the diplomatic relations between the Federation and the Klingon Empire? Prosecution Attorney: There are no diplomatic relations."
 * Klingons try to extradite Worf for allegedly shooting a civilian ship.


 * In that case there is no Extradition Treaty and the episode should end right there.
 * What makes this more ridiculous is that, when the Dominion and Cardassia join forces, Dukat pulls the same thing in regards to a political rival on the station. Sisko pretty much tells him to sod off because there is no extradition treaty between their peoples.
 * The difference is that up until the conflict began the Klingons and Federation were allies and the Federation very much wants friendly relations with the Klingons to resume again. They're playing nice in hopes that it will be a step to reconciliation between their two powers, plus the Federation was not happy with the situation and Worf was hella lucky it was a frame up. Heck, for all we know WORF is the one who accepted the charges set against him and agreed to the trial, murdering civilians would be something all sides could agree would warrant punishment.
 * In my opinion Worf was completely justified in taking the shot. Present day Navies "strongly encourage" everybody to keep well away in peace time. And he was at that time in combat. Anybody who approaches active combat puts themselves willingly at risk. Trying to sneak up on the combatants is suicidal.
 * Plus, ask yourself this: What was a civilian transport with minimal weapons doing with a cloaking device anyway? Those things are extremely power intensive and extremely valuable. The Klingons aren't as protective of them as the Romulans, but that doesn't mean they want anyone to be able to get their hands on one just by bullying the interplanetary version of a Greyhound bus. The fact that the thing was de-cloaking should have marked it as a likely combat target, without waiting to identify it... even if it was a civilian transport that for no appreciable reason had a cloaking device, why the hell was it lowering its cloak in the middle of a fight? Sisko was right to chastise Worf for not pausing at least half a second to at least make sure the shape was right for a Bird of Prey, but he was over the line being as pissed off as he was.

No law against Genocide

 * Sisko's feud with Eddington Sisko genocides the Maquis homeworld. All his officers obey the orders to genocide. And that's it. No pay-back, no investigation. The Federation has no law against genocide.
 * One, there is no Maquis homeworld, they are a diverse set of colonies. Two, he didn't kill anyone, just made the planet unusable for long-term human (and specifically human) habitation. Three, considering Eddington did the same thing with two Cardassian colonies (made them unsafe for Cardassians but not humans), Sisko's zealous pursuit probably prevented the Cardassians from declaring war on the Federation. The Cardassians and the Federation traded the worlds that were attacked.
 * Note that the Maquis colonists are explicitly said to be going for their ships the second the torpedoes hit the atmosphere. They may have thought he was bluffing, but they were ready to run. The Cardassians also had a chance to leave when Eddington made their planets unlivable.
 * If I plant one of those futuristic bombs that do no physical damage except for killing anything alive, and tell everyone they have ten minutes to get out of the blast range, even if they all escape with no problems it's still attempted murder.
 * More like manslaughter, if you honestly do believe no one will be hurt by it.
 * "For the Uniform" has been a controversial episode since it aired, but I think people have a long history of misinterpreting the ending. Sisko did not commit genocide or attempt to -- he just ruined the Maquis's real estate. One might note, however, that he did commit a massive ecological crime, but it seems Starfleet is willing to turn a blind eye to that.
 * Generally if you launch weapons towards a space with the express purpose of making that place uninhabitable by the residents until a terrorist surrenders that's going to at least be ethnic cleansing.
 * Really twisting yourself into a pretzel to reach that one. Sounds more like you're just bound and determined to see Sisko as a slavering, mindless, hateful terrorist and aren't going to let a petty thing like the actual content of the episode in question get in your way.
 * Speaking of Eddington, of all the ships in Starfleet they could have sent after him, why did they pick the one ship he had served aboard to catch him? While this was justified in "For The Uniform" by having the Maquis damage the only other ship in range, Sisko had apparently had the assignment for eight months before that. Did it really not occur to them that, in the months he was aboard, he might have sabotaged the Defiant like he did the station? And surprise surprise, it turns out he did!
 * True, and why give Sisko the job of tracking him down at all? A: Sisko's plate is pretty full anyway, and B: Sisko harbours a personal grudge against him and that threatens his objectivity.
 * The Defiant was apparently one of the few major combat vessels the Federation had in the area (not that it makes any sense to have so few there). Of course why the head of the most important space station in the region is going terrorist-hunting instead of delegating to his officers is a good question.

If You Prick a Changeling, Does He Not Bleed?

 * Throughout the Dominion War people show they aren't changelings by bleeding. This test was first suggested and implemented . Heck, Sisko's father, a chef, figured out how to fool that test as soon as he heard about it.
 * Your point? By the very evidence you supply you seem to get the writers' point right across - that the test . The very episode in which, as you say, Sisko's father points out the fallacies in the test, was meant to indicate this very plot although it wasn't until much later that.
 * More evidence that it's a Batman Gambit? The Martok changeling isn't the first one to come up with the idea of blood tests -- in the episode "The Adversary", Odo notices Sisko can't be a changeling because he's bleeding. But why is Sisko bleeding? Because a changeling hurt him, knowing he'd meet up with Odo soon, and Odo, being a sharp investigator, would notice and develop the blood testing strategy. So, by the time the Martok changeling strolls onto the station, pulls out a knife, and slices his palm open, they all accept it without questioning how or why Martok knows to do such a thing -- they just assume he knows because of the intelligence shared by the only trusted person in the alpha quadrant who could have come up with the idea -- Odo.
 * Come to think of it, it'd be pretty easy to get around that test if you knew ahead of time you'd be taking it. And by making it standard practice, you know when to expect it.
 * It would be a hell of a lot harder if the Feds did a DNA test on the resulting blood which probably takes less than a minute with their technology, that would at least limit the infiltrators to having to always impersonate the same person
 * Going into the morality of accessing everyone's medical records like that might have been a bit too much for a set of episodes that was already rather heavy on the sociological morality navel-gazing. As it is, there were already several segments that were close to the characters just sitting around talking about things for long stretches of time. It's an interesting subject but possibly a little much to ask of a mainstream primetime audience to sit through.
 * Two Words: Security Theater

Good Luck With That Trapped on a Deathless War World Thing!
"Shel-la: Leaving without us? Bashir: My analysis of the microbes that keep you alive showed that if you were to leave the moon, you would die... Shel-la: So there is no end. Bashir [turning to Sisko]: Commander, I find myself caught in a moral dilemma. As much as I'm dedicated to the preservation of life, I wonder if we shouldn't help these people end this torture... Sisko: How could you do that? Bashir: Anything that can be programmed can be reprogrammed. If I can disable the mechanism in these microbes, they would no longer function when someone was killed, and these people would finally be allowed to die. Shel-la: You've seen our lives here. Please... it's the only solution left. Give us a way to reprogram these microbes, and it will mean the end of this war. Kira: You really think the fear of death would stop the fighting? It never has in any other war."
 * Deep Space Nine episode "Battle Lines"
 * They discover a planet with the mysterious power to provide eternal youth and immortality. Its inhabitants have for centuries lived a life of unceasing fear, violence and despair. They were jailed there centuries ago as part of a plan to make their existence an approximation of eternal Hell. Everyone there wants to leave. In the course of the action, the highly-revered religious leader of one of the Federation's most important allies is stranded there. The only thing separating the planet from the outside world is an aging automated satellite defence system.
 * Starfleet Response: Who cares? Let the fuckers rot.
 * Said satellite system is also the only thing keeping those inhabitants alive.
 * Starfleet began working on a way to get them out of there without killing them, but it was never brought up in the series again.
 * The planet is in the Gamma Quadrant, which just happens to be enemy territory for the second half of the show. Even if anyone has the time and resource to come up with a solution, there'll be a minor problem in testing it out or implementing it, if you catch my drift.
 * They left Opaka behind because they had no way to get her off-planet without killing her. And even if they had, she seemed to have decided that bringing peace to this world was her destiny. Kind of a noble sacrifice.
 * A good thing Kira was there, though. The Bajoran government would likely have been pretty pissed off and suspicious if an all-Starfleet crew came back and said "Yeah, she told us to tell you she's staying behind. You'll have to take our word for it." Bajor was still somewhat uncomfortable with the Federation at that point, and something like that would have been a major, major problem if the government's own chosen liaison officer couldn't verify Starfleet's story.
 * They have recording devices and, more importantly, Opaka's still there and able to be talked to (if you manage to get past the satellites to risk beaming someone down). They could have just told the Bajorans "If you don't believe us, go ask her yourself. We'll even show you how we got past the satellites to beam back up." It's entirely possible Bajor did that anyway, possibly sending some of their best scientists and/or doctors to try and work on a solution (assuming Opaka didn't send them right back).
 * The original poster seems to have neglected this conversation towards the end of the episode:

"Shel-la: No-- but it will allow us to finally win. Wipe out the Nol for good. [We cut to Bashir's astonished, disgusted reaction.] Shel-la: On this world, your disabled microbes would be the ultimate weapon, Doctor-- one that we could use to truly destroy our enemies."
 * The following is the Wham! Line here:


 * So the point here is: They didn't disable the microbes because the Ennis and the Nol-Ennis would simply use it as an excuse to finally annihilate one another. They had no interest in making peace with one another, and that's why Kai Opaka willingly stayed-- to help them begin the healing process. (In the Expanded Universe, the two tribes eventually )
 * That makes sense - when they had the benefit of immortality, if not for the war, they would have had plenty of time to develop scientific processes necessary to not only understand the microbes, but alter them. It is possible that it was, in part, a component of the plan of those who imprisoned them there to begin with - their fighting would continue until they had eventually learned the futility of it, and started to actually work together. Eventually, they would come to develop the technology necessary to end the cycle completely and escape the moon, but it could only happen if they first end their war with each other, and since both sides were made immortal, war could not be ended by the victory of one side over the other - only a diplomatic ending was possible.

Good Luck With That Cardassian Prison Thing!

 * Deep Space Nine episode The Homecoming: Kira and O'Brien go to break Bajoran prisoners out of jail. Good so far. They can't use the transporter to beam them up because the runabout's transporter can only beam two people at a time and there's a dozen, so beaming two of them will make the guards fire on the rest. Makes sense so far. They land, make a daring escape with six of the prisoners, get to the runabout and fly off because the guards are firing with hand weapons. Then, even though no one is shooting at them with weapons rated for ship fire, they raise shields and fly off leaving 6 of the prisoners to die instead of beaming them onto the ship! What the hell?
 * They have to leave in a hurry because there are two warships coming into range; they may just not have had the time.
 * Correct. Locking on to someone and beaming them up takes a bit, and the warships were essentially right on top of them.

Changelings Fail Kidnapping Forever

 * Another Deep Space Nine episode, "The Adversary": It's a "find the clone among us" plot with Changelings, and we're told the Changeling is Eddington. On leading him to the brig, we find out  But why the hell would the Changeling
 * It wasn't
 * In addition,

Don't Mess With the Ferengi Commerce Authority!

 * The existence of the Ferengi Commerce Authority really bugs me. Remember the Liquidator who somehow had the authority to come on to Deep Space 9 (a Federation outpost), shut down Quark's bar and threaten to sell all of his financial holdings because of his Mother's actions? How can they possibly have that power?
 * Well, even though Quark's is on a Federation outpost, the Ferengi are not a member of the Federation. Nog couldn't even join Starfleet unless Sisko sponsored him.
 * Quark is working under the authority of the Ferengi Commerce Authority. Regardless of where he works, he still has to operate under Ferengi law to keep their authority. Without their authority he cannot do business with other Ferengi. They have every right to revoke his license and take any other actions required under Ferengi law. It's like if you work for an American company in Russia. Your company can revoke your ability to do business with them there. (The Ferengi Government is more like a corporation than a government if you recall).
 * Plus, it's not a Federation outpost. It's a Bajoran outpost with a Federation administration.
 * It's not unprecedented for a government authority to have the ability to reach your assets in another jurisdiction. If you're American, you're a prisoner of the IRS wherever in the world you go. This is not true in most countries' tax systems, who only tax on money earned inside their borders.
 * Because his financial holdings are only recognized by the Ferengi government. The Federation can't stop Brunt from selling off Quark's assets because those assets ''do not exist" as far as the Federation is concerned. It would be like the United States trying to stop Switzerland from seizing the assets of a Swiss tourist.
 * At the end of the episode, he re-opens the bar and continues doing business after Sisko &co. donate furniture and resources (for the community's benefit). The FCA can stop him trading legally with other Ferengi, but have no power to stop him running a business in Bajoran territory, so they don't. (Let's just assume that the Ferengi staff are now formally employed by Sisko or something.)
 * Actually, for the duration of the revocation of Quark's business license, no Ferengi are seen working in the bar. Presumably he hires extra dabo girls, who then pull double duty as waitresses.
 * Doesn't its very existence go against the Ferengi principle of free enterprise anyway?
 * DS9 was the first series to really develop the Ferengi, and did so by taking them out of the "pure fantasy" realm of Star Trek where societies actually could be purely one dynamic (such as the fantasy that the Federation was a "pure and proper" communist utopia). The Ferengi aren't pure capitalists because such a thing is effectively unable to really exist... humans, and therefore by our judging sentient beings with society, want some form of order and structure, and will eventually create these. Thus the Ferengi have created a sort of mish-mash of capitalism and statism where everyone's highly capitalism-focused but it's effectively impossible to produce anything or have a business without going through the government.

Whacking the Dominion Hive

 * In the Deep Space Nine episode "The Jem'Hadar", a Jem'Hadar representative of the Dominion comes through the wormhole and states, in essence, that the Gamma Quadrant (or at least the part of the quadrant near the wormhole) is within Dominion space, and that any excursion through the wormhole would be considered an incursion into their territory and treated as such. The general response on the part of the Bajorans and Federation is basically, "Oh, yeah? Try and stop us from exploring!" Why the sudden disrespect for the requests of a sovereign nation? If the wormhole instead led to, say, an unexplored mass of space within Romulan borders and the Romulans sent a representative that said, "Quit sending ships into our space!" would the Federation thumb their nose at this, or would they back off and resolve the matter more diplomatically? But no, the Federation and other Alpha Quadrant races keep sending their (heavily armed, at least in the case of the Defiant) ships through, completely disregarding the wishes of the Dominion. No wonder the Dominion finally just decided to invade the Alpha Quadrant itself.
 * If I recall correctly, the area around the Gamma Quadrant terminus of the wormhole wasn't Dominion territory for the first two years of Deep Space Nine. Certainly most of the people we met from the Gamma Quadrant in those two seasons seemed to treat the Dominion as an abstractly distant power rather than as an aggressive occupier. It seems more like the Dominion unilaterally annexed that territory around the end of season 2, then barged through the wormhole and told the Alpha Quadrant to GTFO. Since this was Kira they told this too, she naturally wasn't going to take this lying down. It should also be noted that the Dominion asserted their authority in their new "territory" by hunting down and destroying every single Alpha Quadrant ship and colony they could get their hands on.
 * The wormhole terminus was never really part of Dominion territory. I believe the writers used a metaphor something like this: Imagine if the Chinese claimed complete dominion over the East China Sea and added that ANY non-Chinese ships there would be destroyed. Yes, people wouldn't start sailing on the Chinese coast, but they wouldn't really pay any attention to this warning on the coast of Japan or even some distance away from it. One single navy couldn't possibly patrol a region so vast, and the Federation knows that the Dominion is only a distant threat in the section of the Gamma Quadrant they're near, so they keep exploring and don't really get caught.
 * The Federation is a great power in its own right, and even peaceful great powers don't like being bullied. Even weak governments don't like that. The Dominion's demands were a slap in the face of Federation sovereignty.
 * Both the phrase "Whacking the Dominion Hive" and this complaint, by the way, come straight from Phil Farrand's The Nitpicker's Guide for Deep Space Nine Trekkers, a book full of Headscratchers and other nitpicks. 'Tis a good read.
 * Only in Star Trek fandom would people suggest an entire book's worth of sitting around and nitpicking to be a good read, I've gotta say.

Attack of the 50-Foot Odo

 * So Odo's a changeling, right? We've seen him get pretty small, and change his mass so, for example, when he's a bag he's not as heavy as his humanoid form. This means he can change his mass at will (which is a Headscratcher in and of itself). We've also seen Changelings flying through space on their own without any problems (like Laas did in "Chimera", as a creature the size of a runabout). Why doesn't Odo ever use this to his advantage? Why does Odo take runabouts when he could just go into space by himself? Or, for that matter, why couldn't he become the size of the station and just pick up enemy ships and hurl them into the sun or something (other than it would be totally ridiculous)? They wouldn't even have needed to do effects shots: just shoot Rene Auberjonois handling the actual ship models used for filming! True, it would be pretty silly, but I think there are other possibilities to use a giant Odo (humanoid or not) or at least a spaceworthy Odo that would've been useful and cool to see without treading into B-movie territory. But I think the only time we ever see him get larger than his humanoid form is when he is protecting "Kira" from a rockfall in "Heart of Stone", at least that I can remember.
 * I agree in the abstract that Odo does not use his powers usefully very often. On those odd occasions when he forms tendrils to grab attackers, I wonder why he doesn't do it more. But do not forget that, in the grand scheme, he is a novice changeling. He was amazed to find that Laas could fly through space as this was a power well beyond his, so one can't expect him to just be able to do it himself. This is an important part of his characterization -- remember that Odo is a misfit, not a demigod. Laas had centuries of practice that Odo lacked, and the Changelings in the Great Link had significantly more again.
 * Odo does become significantly larger than his humanoid form in "The Alternate," but does not do so consciously, again an indication that he has vast powers that he has not begun to master.
 * Further, note that the Changelings tend towards using their powers in subtle ways for purposes of infiltration and subterfuge, rather than spectacular shows of force. What would be gained by becoming giant, even if they could do it? Changelings are not invulnerable, and it would just provide a larger target.
 * From a real life perspective it could easily have been because all the shape shifting could be expensive and difficult to do.
 * I just want to know what happens to his comm badge when he turns into, say, a drinking glass (as we see one episode.)
 * He met Laas before "Treachery, Faith and the Great River", so I'd personally like to know why Odo was concerned about freezing to death or asphyxiating in the latter episode. He knows for a fact that Changelings Can Breathe in Space!
 * Laas can also turn into fire, so that may be how he keeps warm in his space-dwelling form. And maybe he just held his breath. If he can travel faster than light then anything is possible!
 * Um, "Treachery, Faith and the Great River" was eight episodes earlier than "Chimera."

Why was Odo turned Human and not Bajoran?

 * Why did the Founders in the Link make Odo anatomically human (as Bashir's analysis confirms) and not Bajoran? He has far greater ties to the Bajorans than the Federation; he was raised by a Bajoran scientist, he's part of a Bajoran security force, and the whole basis of the female changeling's accusations about his divided loyalties are based on his, who is Bajoran. And the Founders don't seem to be sensitive to the fact that humans are a major force in the Federation; they don't make too many distinctions among species of solids anyway. But if they were going to choose a specific species to turn Odo into, the logical choice would've been Bajoran.
 * It is a curious decision, which reeks of the Star Trek's humanocentric sense that everyone who isn't human should strive to be... or become one involuntarily! But justifications as possible. For the Founders, it's an us and them mentality, as you note: solids are solids. So perhaps their choice was arbitrary. Perhaps they had examined more humans and knew their anatomy better. The "Odo as human" arc turned out to be a bit of a Dork Age, didn't it?
 * Could have been another layer of the punishment. By turning Odo human, he is further isolated from the culture that he grew up in and is thus made even more alone.
 * I'm not sure that really works as an explanation, because 1: Odo was only marginally connected with Bajoran society to begin with, and 2: he doesn't outwardly look like a Bajoran even during his exile. He just looks like Odo (and, as emphasized in "Apocalypse Rising," chooses to continue to look that way). The arrangement of his internal anatomy would seem to make little difference.
 * Honestly I always just assumed when Bashir said "He's human" he meant "He's a solid, organic creature with most of the organs we're familiar with". On the other hand, if he was literally human, the Founders may have studied human anatomy much more closely than Bajoran because of their infiltration of the Federation.

A bit quick to profile there

 * In Field of Fire why is Ezri so quick to assume that the murderer must be targeting people who are laughing in their photos? For that matter, why is she so quick to assume that  it was a Vulcan murderer? For all she knows it could have just as easily been a professional from a completely different species who had been sent after specific targets.
 * And the heck of it is, she was right. Of course, it wasn't just her coming to that conclusion; Joran helped quite a bit.
 * Because she could find literally nothing else that bound these people together. A professional made even less sense because these weren't people that there was any possible reason to hire a professional to kill. The whole difficulty with the situation was that there was no apparent logic to the murders. And she explains why she makes the assumption it's a Vulcan in the episode... just like all this other stuff is explained in the episode. So 1) rewatch something and actually pay attention before making a headscratcher, and 2) spoilers are really pointless on a headscratchers page and it's specifically stated that you don't need them.

New Bajoran Prisoners As the Plot Demands

 * In season 2's premiere "The Homecoming", while discussing with Dax whether he should give Kira the runabout to go rescue Li Nalas, Sisko asks, "Suppose I give her the runabout and she does rescue Li Nalas. What do I say to the Cardassians?" Dax replies, "The question is, what do they say to us? They swore they released all their Bajoran prisoners." Now, of course, Kira rescues Li, and it turns out they have a dozen more Bajoran prisoners in that prison camp on Cardassia IV, which Dukat has released, probably to save face. (Because I do not believe him when he says the Central Command was unaware of the presence of those prisoners. They're not that stupid.) So presumably all the Bajoran prisoners detained by the Cardassian government were released then and there. Yet, later that season the Cardassian government agrees to release six Bajoran prisoners in exchange for Natima Lang, Hogue and Rekelen. What Bajoran prisoners?! And then in season 3's "Life Support", we learn explicitly that Cardassia is withholding certain detainees which they hadn't previously mentioned.
 * Actually, this is totally in character with Cardassian society, military, and morality. The Central Command only admits to crimes when it's been caught. It's no surprise to me that years after the Occupation ended, the Cardassians could still be holding Bajorans prisoner. They're Cardassians, the Space Nazis of Star Trek.
 * Not to mention, this is playing off of real-world incidents. For example, the Soviet Union held on to German POWs for years after the war ended. There's also persistant (though entirely apocryphal) stories about American POWs still being secretly held by Vietnam or China after the Vietnam War.
 * Original Poster: But that's exactly my point. Since the Cardassians have already promised that they released all their Bajoran prisoners, the Federation and Bajor should take a more hard-line stance when Cardassia attempts to negotiate with the release of (allegedly nonexistent) Bajoran prisoners. Their governments should say, "What Bajoran prisoners? Your government already agreed to release all of them, and we demand that you live up to that agreement."
 * I agree; this is a simple continuity problem.
 * Isn't the problem with the government saying that the risk that the Cardassians would just go "Oh, I guess you're right, sorry, there really aren't any more Bajoran prisoners. Or at least there won't be tomorrow."
 * It could have been a one-time amnesty at the end of the occupation; the Bajorans captured later would be members of the Maquis or other terrorists that carried on the fight after the occupation was over. Though they may be criminals, Bajor would want their citizens back because their government knows full well how harshly Cardassians treat their prisoners.
 * It could have been that the Cardassians were releasing all political prisoners in that agreement, and later prisoner releases were for crimes such as murder, theft, etc. that took place under the Occupation. Or prisoners taken since the end of the Occupation for things like border incursion, smuggling, or espionage.

Duh, the Cardassians just want the station

 * And speaking of "Life Support", why are Sisko and Kai Winn so mystified when Legate Turrel insists on an agreement in principle that anything of Cardassian origin left behind in the Bajoran system belongs to Cardassia? Duh, the Cardassians just want the station! And the de facto control of the wormhole that comes with it!
 * Probably because if the Cardassians really wanted the station back, Starfleet could just hard wipe the computers, push it over the border into Cardassian territory, and set up a new space station outside of the Wormhole, since the Wormhole's in Bajoran territory. They wouldn't get the territory just because they got the station back.

The General's Kia-of-Prey

 * For much of the second half of the series, General Martok is hanging around the station in one capacity or another, and has command of the Rotarran, a Bird of Prey, which eventually becomes his flagship as he is given command of the Federation-Klingon fleet. Wait, what? Why is a tiny, hundred-year-old skirmisher with a crew of cowards and rookies 1) appropriate for a General, 2) appropriate to act as flagship once said General has been given a proper command again, or 3) a sensible choice of vessel for a man whose family apparently owns a private attack cruiser, a powerful modern vessel representing the best of Klingon ship design?
 * Because he feels a Bird-of-Prey is a proper vessel for a Klingon warrior, far better than the "luxury liner" of a Vor'cha- or Negh'Var- class attack cruiser. When he was promoted to the liaison officer between the Klingons and the Federation, he declined Sisko's offer of quarters aboard the station, saying, "I will keep my flag aboard the Rotarran. At least then I'll feel like I'm still in the war." In other words: It keeps him grounded. I must admit, though, that you're right that it doesn't make much sense from a strategic perspective. Three or four well-placed photon torpedoes would destroy the general's flagship.
 * Simply because the basic external design is 100 years old doesn't mean the Rotarran is a century behind in technology. The Klingons are really fond of that design and seem to upgrade everything under the hood so it can fight against 24th century ships. They are either still building new ones or they're upgrading them the same way the Federation upgraded Mirandas and Excelsiors to be a match for Dominion ships. Another important question is whether the Rotarran is a B'rel-class scout or a K'vort-class cruiser; the latter is larger, better armed and can probably take more of a beating. As for why not command from a more powerful and distinctive warship, it could be that if the Dominion knew Martok were on the only Negh'var in the fleet they would make it a priority target, whereas if there are scores of Birds of Prey in any engagement it's much harder to identify which one Martok is on. It keeps the Dominion on its toes: if they get a report that a squadron of Birds of Prey is going to attack some depot, they don't know if its a bunch of hotheads or the General and won't know how to properly allocate defenses. Contrast that with if they saw a Sovereign-class coming they'd know it was Picard.
 * Regarding his crew that keeps ending up filled with rookies, I can think of at least three reasons why it keeps happening: 1) He got out of a Dominion prison camp after being replaced by a Changeling, so he hadn't re-earned the trust of Klingon veterans yet (backed up by the fact that we only see his crew after he was recently released), 2) he really is a good trainer, general or not, and one of his duties is to train rookies simply because he's the best at it (admittedly this has little proof), or 3) Gowron doesn't want to see him get too popular and so keeps sending him inexperienced crews to hinder his progress (this one's especially backed up by Gowron's behavior near the end of the series).
 * Given that Martok wasn't originally a highly-placed member of the Klingon society, it could be a sign that he considers his humble origins to be a source of honor, and this uses a more humble ship that the large cruisers that the other generals use. Also, there are numerous stories of Generals who will fight alongside their men and end up earning their loyalty, as opposed to those who lead from the rear and merely have obedience (compare General George Patton and General Max Taylor from World War Two).

Jerk refuses to help? No higher authorities.

 * In the episode Babel the station has been completely shut down by an old Bajoran-engineered virus that not only causes aphasia but also seems to be lethal if untreated. Kira manages to find a doctor on Bajor who might have some knowledge of it but the moment she brings it up he cuts off communications. Her response is to kidnap him and force him to help them find a cure. It never once occurs to anyone to contact the Bajoran government, explain the situation (including the many infected Bajorans) and ask them to send him to help? For that matter, couldn't the Bajoran government threaten the doctor with prosecution over his negligence? Is force and deliberately infecting him really the first thing that goes through Kira's mind?
 * Kidnapping is generally faster than dealing with red tape, even the emergency services.
 * This is an early first season episode - Bajor is still recovering from the aftereffects of the recent Cardassian occupation and withdrawal and it's likely that the provisional government isn't sufficiently established to be able to help here. It's also consistent with Kira's personality that she would take the direct approach over appealing to whatever authority might exist.

As long as it's all a game laws don't matter

 * In Move Along Home the Wadi force Kira, Sisko, Dax and Bashir to be game pieces in Quark's game, at times making them reasonably believe that their lives are in danger. At the end of the episode Sisko starts to call them on this before Odo advises him to get the full story from Quark. Even though Quark did unwittingly help cause it that doesn't change the fact that the Wadi abducted several officers. So are we supposed to feel that as long as Quark gets yelled at and the Wadi explain that they never had the four in real danger it makes the crime go away? Would Sisko tolerate it if they did this again?
 * Diplomatic immunity?
 * Exactly. Seriously, what do you expect Sisko could do? Arrest them? Expel them? Kick the first formal visitors from the Gamma Quadrant off his station because they made him think he was in personal danger? I'm amusing myself by picturing Admiral Nechayev's reaction that decision! Sisko's reaction -- "that was weird, but let's put it behind us" -- is the only one possible.
 * If they had put a gun to his head and then revealed that it was fake I doubt he would have been so forgiving.
 * And? They didn't put a gun to his head. And try this on for size: the Wadi well and truly did not seem to understand that anyone wouldn't want to take part in their game. They misjudged their audience (as did the Iyaarans in Liaisons) but when cultures are interacting for the first time, this is a known risk.
 * Sisko's the guy whose first reaction to the Wormhole Aliens declaring him evil and suggesting he be wiped out of existence was to attempt diplomacy. I don't think a little bit of rough treatment was enough to shake that outlook 100%.

State-sponsored murder has no consequences

 * In Armageddon Game the T'Lani and Kellerun decide to help each other bury all knowledge of a biological weapon by killing everyone involved in dismantling it, including Bashir and O'Brien. Ignoring the fact that they thought they could murder two officers from the regional superpower they then try to murder Sisko and Dax when they attempt to rescue the two. By this point it's clear that at least an important Federation officer is aware of the attempted murder and the two races could reasonably infer that his officers would know where he went and what his suspicions were. Did they really think that they could just cover this up too? Were they really certain that the Federation wouldn't consider retaliation? For that matter their motives make no sense. They offer to let Sisko and Dax go if they hand over Bashir and O'Brien because they just want to kill anyone who had knowledge of the weapon. If they really can't trust the Federation to never make use of the weapon then murder won't change anything, the Federation easily has enough resources and expertise to make its own.
 * Another horrifying thought: Given the length that the T'Lani and Kelleruns were willing to go to to prevent knowledge of the harvesters from continuing to exist... who's to say that O'Brien and Bashir were necessarily safe once they arrived back on the station? Did they have to look over their shoulders the rest of the lives?
 * Probably not. Now that the Federation knows what they wanted to do, trying it again would give them worse things to worry about than a few biological weapons here or there. And Bashir and O'Brien are unlikely to return to T'Lani or Kellerun space of their own accord, or even talk to their representatives, so the knowledge won't be returned to the people who are interested in it.
 * The T'Lani and Kellerun were certainly willing to attempt murder when there was no reason to think that O'Brien and Bashir would return anyway. Really the only way they could be safe would be a very large warship reminding both species why the Federation is one of the dominant powers in the galaxy.
 * This is most likely the answer. The Federation most likely calmly, diplomatically explained to the T'Lani and Kellerun that they'd committed what amounted to an act of war, which the Federation would kindly overlook, but if anything ever happened to Bashir or O'Brien and it got traced back to them, they'd stop overlooking it.

Off-screen, never mentioned before war crimes?

 * In Waltz Sisko is transporting Dukat to Earth so he can be investigated for war crimes. What war crimes? Pretty much everything we saw of him during the war suggested he was rather restrained and making an effort to be reasonable. If they're referring to his occupation of Bajor then why isn't he being tried on Bajor? In Duet Sisko had no problem allowing the clearly biased Kira investigate a man pretending to be a Cardassian war criminal.
 * I'd assumed "investigated for war crimes" was code for "tie him up in enough red tape 'preparing' for a trial that he can safely be imprisoned without charges until the war is over".
 * That sort of thing usually got at least some discussion on the show, even if it was just to state that this was the least bad option. Even if we assume that a de facto imprisonment was the unstated goal, it still doesn't explain why he wasn't handed over to Bajor. There a conviction and execution would be guaranteed. It feels like the writers thought that Dukat was getting too popular.
 * That guaranteed execution might be part of why the Federation would have been reluctant to hand him over to the Bajorans...
 * There's also a big difference between what we saw of Dukat, as viewers, and how much the Federation knows. We know that he was actually pretty restrained because we saw it happen, but the Federation would realistically need to carry out an investigation to sort things out, which is what they were doing now that they had him in custody. Plus, I'm sure "investigating" Dukat's role in the Dominion War is, in part, a way of trying to get him to cooperate and provide them with valuable intelligence.
 * Dukat claims he was very restrained and attempting to help the Bajorans. Dukat is not a trustworthy source of information on Dukat, as by Word of God he's a delusional narcissist who convinces himself he's the hero. (Remember, he eventually admits that he actually hated the Bajorans and wishes that he'd, quote, "killed them all". He still wanted them to love him despite this, showing just how bad his narcissism was, he wanted even the people he despised and considered worthless to love him.) Also in Duet Kira was the one investigating a war criminal because the (alleged) war criminal was arrested by a Bajoran security officer on a Bajoran station for crimes committed on Bajor, whereas Dukat was apparently apprehended by the Federation and was going to be investigated for his crimes in both the Occupation in general and probably other matters related to it.

Cloning a man as evidence?
This has been bugging me ever since I saw "A Man Alone". Some funny genetics are found amongst the skin flakes of a murder victim's room. Bashir then clones the genetics to see what it is. Fair enough. But even when he realizes it is developing into a humanoid (and a fully grown one at that), he continues the experiment until there is a fully adult clone living and walking around. Is creating a new lifeform as part of a crime investigation really all that ethical? Especially considering this person will have a drastically shortened lifespan, and will have to learn even the most basic things. Yet no one seems to even remark on this.
 * To be more precise, he cultures the material, which then begins growing by itself. He wasn't trying to clone it, it was a self-growing clone. All he did was unintentionally give it the means to grow. Once it grew to the point that it was clearly humanoid, it would have been unethical for Bashir to just kill it out of hand.

more about Dax's extradition
Okay, so there are four possibilities: 1. The trill are not a member of the federation, and Dax is not a citizen (which could be possible, seeing as how starfleet is a scientific organization first, and a military second). 2. The trill are a member of the federation, but Dax is not a citizen. 3. The trill are not a member of the federation, but dax is a citizen. 4. The trill are a member of the federation and dax is a citizen. That means that in every case, either Dax couldn't be extradited, or there would have to a law already established.
 * In that case, the Klaestron would have been unable to extradite her.
 * She wouldn't be a citizen, so they couldn't extradite her AND the federation would have to have established whether a conjoined trill is a single person or multiple people.
 * In that case, she should be registered as either a single person or as two people. If she is registered as a single person, she would obviously count as a single person under federation law and not be extradited.
 * All of the above.

The head of a space station only a commander?

 * This has always bugged me about Deep Space Nine. When the series starts, Sisko is a commander, only getting promoted to captain during "The Adversary". But shouldn't a space station have a higher ranking officer? It's larger, so probably needs more people to properly maintain. It's a political symbol of the federation, and the commander will be required to negotiate in its name. And, it's the docking place for other federation ships, which are led by captains, which could cause chain of command tension in a crisis.
 * I don't know about other Federation stations, but DS9 was somewhat of a special case. At the beginning of "Emissary", Starfleet wasn't completely taking over the station, but helping out Bajor after the occupation as a facilitator. The Starfleet crew early on was nearly a skeleton crew: you had your doctor, your chief engineer, your head science officer, and a few other crewmen scattered here and there to fill gaps, but the rest of the station personnel were mostly members of the Bajoran militia (such as Odo's entire staff). This wasn't exactly a plum assignment, or even much of an important one; Bajor wasn't strategically important, the station wasn't exactly a major hub for starships, or any traffic, for that matter (remember, it wasn't named Deep Space Nine because it was in a major traffic zone), and the station was still technically Bajoran with a token Federation presence. Perhaps Starfleet just didn't see it as important enough to send a captain in. It was only after the discovery of the wormhole that suddenly Bajor and the station became important to both the Federation and the Alpha Quadrant as a whole, but by then Sisko had already been placed in the position of Emissary by the Bajorans, and the Starfleet higher-ups probably thought it would weaken their relationship with Bajor to bring in somebody else above Sisko at that point.
 * No doubt Sisko has special training and experience that makes him appropriate for such an administration job (and it's easy to forget that, at the beginning of the series, Sisko is a mid-level administrator). I think spending so much time aboard starships throughout most of Star Trek fosters a "captain or nothing!" mentality in most audiences, but realistically a commander is more than experienced enough for most command situations.
 * Even before Deep Space Nine started, the EU had established that starbases were generally overseen by Commanders. It's considered an administrative position designed to get someone used to paperwork and some amount of drudgery mingled with a certain amount of autonomy and being in command, as the final seasoning some officers need before being promoted to Captain and given their own ship.

Vital ability to see tiny indistinguishable specks?

 * In A Time to Stand Jadzia treats the absence of a viewing screen on a Jem'Hadar ship as an inexplicable flaw in the design. What exactly does she expect the screen to do? The ship's sensors would 'see' anything long before the crew would. In comparison the complaints about a lack of seats, replicators and medical facilities are much more intelligent.
 * Persistent, deep-running streaks of bad writing throughout the franchise have established that for some reason ship sensors can't pick up all of the same details that a viewscreen can, and that magnifying the viewscreen can actually get you detail beyond what the sensors can resolve. How this makes anything even approximating sense is anyone's guess... perhaps Federation Engineering strikes again and visual data actually uses a whole second set sensor system with a much higher sensitivity than the important ones (the real surprise for the characters perhaps being that the Jem'Hadar ship was designed in a sensible fashion in this respect).
 * It makes perfect sense, actually. It's quite easier to get a sense of what's going on with a visual than streams of numbers. Any being with eyes would process a visual far more efficiently than a readout on a console. If there's an enemy ship ahead, your weapons officer will have an easier time targeting if they have something to coordinate with rather than just a hit/miss return.
 * Considering the distances the ships would logically be at and the fact that we never see anything like a targeting system on the screen it doesn't seem very likely that it would be of any help. Besides, apart from an apparent lack of tactical imagination there is never any guarantee that the enemy won't be below or above them.
 * The viewscreen has the ability to create simulated images. It may be the viewscreen is normally used to produce an image based upon sensor data in the same way the Jem'Hadar headsets do (it's not as though it's the headsets themselves give the wearer X-ray vision, after all).
 * It's important to remember that one of the most common Trek uses for such a viewing screen is to facilitate face-to-face communication and diplomacy between ships, allowing for added nuances of body language that are otherwise lost via voice or text. The Jem'Hadar, naturally, do no diplomacy on the part of the Dominion; that's the Vorta's purpose, so there's no need for such a thing on a Jem'Hadar warship. In that light, the comment is a reflection on the mentality of Jem'Hadar ship commanders.

"We're better"

 * One of Quark's best scenes comes in "The Jem'hadar," when he turns Sisko's Federation highhandedness back on him: "You're overlooking something, Commander. Humans used to be a lot worse than Ferengi. Slavery, concentration camps, interstellar war; we have nothing in our past that approaches that kind of barbarism. You see? We're nothing like you. We're better." It's a great example of how DS9 calls out Star Trek as a whole on its often hypocritical values. But does it really make sense? The Ferengi hardly have a great record on gender, and we have seen in other episodes that they do indeed practice slavery -- maybe not of other Ferengi, but what difference should that make? And as we see in "Business as Usual," some Ferengi seem to have no trouble abetting genocide, so long as there's a profit in it.
 * I think you may have answered your own question, at least to a point. Unlike humans, the Ferengi haven't enslaved their own kind, which to them may be morally inferior to just slavery in general, and perhaps they don't believe that enslavement of other species is slavery at all. And abetting genocide isn't committing genocide. True, they're both morally bankrupt and reprehensible acts, but the minor differences may be enough for Quark to convince himself of Ferengi superiority (which he does, right up to the end of "Business as Usual", and that's mostly because of the scale of that particular slaughter, rather than the act itself). Whether he's right objectively is another matter, but I believe that at least Quark can justify it to himself (keep in mind that Sisko's reaction basically amounts to "You have got to be kidding me.").
 * History is written by the publishers. It's just as likely the history books detailing the slavery and warfare perpetrated by the Ferengi just don't sell as well as the ones that never question the wisdom of the Rules of Acquisition.
 * I wouldn't deny that it probably all makes sense in Quark's mind. But for me at least, subjecting these claims to scrutiny weakens the overall dramatic impact of the scene.
 * That could be the point. Quark goes on about how the Ferengi are better than hew-mons, but in reality the Ferengi have the same flaws that Quark denies. Consider how we tell ourselves today that we are better than our ancestors from even just a few generations back, and then compare our mental image with the reality in the streets.
 * This misses the primary point. The Ferengi are Blue and Orange Morality, but they stick to that. Humans say genocide, slavery, etc. is bad, but did it for thousands of years. Ferengi said not making profit is bad, and (with only small individual exceptions) held to that. This would be similar to only a few cases of fights in the history of human civilization. The point is the Ferengi stick to thier moral code, humans don't.
 * You can't call hypocrisy on an entire species. Especially not when the moral values you claim humans don't stick to didn't even exist for most of our history.
 * No, and furthermore, Quark does accuse humans of hypocrisy, but it's along the lines of "You think you're better than us but your horrible history reveals otherwise," not "we are at least consistent in our values." It's simply not what he says. Other DS 9 episodes try to redeem the Ferengi along the similar lines (I recall an episode where Nog suggests that the Ferengi could end the Dominion War through their methods by finding something each side wants), but this is a bit of a retcon of the fact that Ferengi were initially presented as a warlike species.

"Or should I say Bill?"

 * Admiral Ross went without a first name for a while, until "Image in the Sand," when Odo says to Kira (sensitive about being called "Colonel"): "Well, has Admiral Ross, or should I say Bill, arrived yet?" Indeed, later episodes call him William or Bill Ross. The headscratcher is that the Deep Space Nine Companion notes that the writers weren't sure at first if that reference was to be taken literally (and early set decorations called him "Cliff Ross"), because it was in the context of Odo cracking a joke. It was indeed gentle dig at Kira's discomfort with her new title, but how could this joke work at all if Admiral Ross's given name was anything other than William?
 * If his name was something else, the joke would have been Odo just picking a "stereotypically human" name to call him as opposed to his actual given name. Maybe there are enough Williams in Starfleet that other races have caught on that "Bill" is something a lot of pale human males are called.

Hastily thought out mole hunt from shaky evidence?

 * In Inquisition Sloan suggests that for most of the episode he had strongly suspected Bashir of being a traitor. However his actions create two problems that really harm the idea of Section 31 being efficient. The first is that the evidence we see isn't exactly strong and hardly enough to go to the effort of kidnapping an important doctor. The second is that if Bashir really had been a traitor his meeting with the fake Weyoun would have tipped him off that this wasn't real.
 * Sloan knew the entire time that Bashir wasn't a mole. He wanted to test him to see if he was worthy of joining Section 31. It's been a while since I've seen the episode, so I don't remember the particular reason it was so elaborate.
 * Slaon mentions that he had been proven wrong by the test, implying he had suspected that Bashir was a traitor before.
 * Simple answer: Sloan is Section 31. He suspects everyone of being a traitor.