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Dr. Franklin is investigating the death of the fourth Markab of "natural causes" in just a few days. He's good friends with the local Markab doctor, Dr. Lazarenn, but even so he finds the sudden deaths a cause to worry. He does a more thorough autopsy of the bodies and eventually discovers that the Markabs died of a plague.
While events are brewing, Sheridan attends a dinner with Delenn and Lennier, repayment for Sheridan taking Delenn to dinner in "A Race Through Dark Places". Unlike their dinner in that episode, this dinner is highly ritualized. Lennier spent two days with no sleep or substantial food in order to do the preparations properly. Eating the dinner is also highly ritualized: portions are exchanged, one can only eat with the right hand, and one must meditate in between each bite. While this scene is played mostly for laughs at Sheridan's expense, we do see that despite his frustration he's making a real effort to reach out to Delenn and learn some Minbari culture. In the meantime, a Markab ship is overdue for arrival at the station, so Keffer leads a wing of Starfuries to investigate. They find the ship with all Markabs onboard dead; they tow the ship back to B5. Sheridan and Franklin meet Keffer as the lieutenant arrives, just in time for Dr. Lazarenn to indignantly protest them seizing the ship without permission. In return, Franklin accuses Lazarenn of covering up a plague, which certainly gets Sheridan's attention.
Now that the truth is out, Lazarenn reveals what he knows to Franklin. The plague is highly contagious and completely terminal 24 hours after symptoms develop. The plague had appeared on the Markab homeworld once long ago, but because of the region where it appeared, it was associated with immorality. Now, to tell a Markab that he's got a plague is to accuse him of being immoral, so the Markab government has completely covered up the current plague, which is worsening on the homeworld rapidly. Lazarenn was ordered by his government not to reveal anything. He doesn't know how the plague is transmitted, nor if it's communicable to other species. One gets the impression that the Markab government hardly allowed any of its scientists to even study the plague.
Sheridan quarantines B5 and orders all Markabs to submit blood for analysis, per Franklin's suggestion. Franklin wants to find a Markab who is in the early stages of the disease so that he can study its progress in hopes of finding a cure or vaccine. Violence increases on the station as other species attack Markabs for bringing the disease onto the station.
The Markab ambassador protests Sheridan's orders concerning the blood tests, claiming that Sheridan is insulting all Markabs by implying that they are unclean. The ambassador says it's the non-Markabs who are unclean, and they will isolate themselves away from the foreigners by moving into one isolated section of the station. Sheridan allows this, even though it seems like it would be within his authority to deny such a mass movement of inhabitants (there are some 4000 Markabs on the station).
Delenn asks that Sheridan allow her and Lennier to join the isolated Markabs in order to bring them what comfort is possible. Sheridan is stricken at the thought, because as he says, he may not ever be able to let her out. (And if the plague is communicable to Minbari, she may be speeding up her own infection.) We have seen Delenn and Sheridan's relationship get stronger, but Delenn's possible imminent death brings out feelings in both of them that they probably aren't ready yet to fully acknowledge. Delenn actually caresses Sheridan's face before she bids him farewell, saying that if she does die, she'll see him again in the "place where no shadows fall". Sheridan doesn't quite know what to do with himself.
I really can't imagine doing what Delenn and Lennier did: locking themselves into isolation with thousands of beings of another species who are all probably going to die. They give blankets and food to the suffering Markabs, but there's no hope for any of them. They help a Markab child find her mother, only to see signs of the plague in her, too. This scene is blatantly manipulating the viewers' emotions, but it's heartbreaking even so.
Dr. Lazarenn has not isolated himself with the rest of the Markabs, but instead turned himself over to Franklin in MedLab to study. He's put in an isolation chamber, and we soon see the symptoms of the plague in him. Franklin also receives the news that the plague has killed a Pak'ma'ra, so it can spread to at least some other species. As Lazarenn's condition deteriorates, he helps Franklin make the connections between the Markab and Pak'ma'ra that finally leads Franklin to a potential cure. It's too late for Lazarenn, but Franklin orders hundreds of doses produces, and he rushes to the Markab isolation area with Sheridan, Ivanova, and Garibaldi.
The door is opened and we find the worst case scenario: all of the Markabs are dead. The stunned looks say it all. Delenn and Lennier pick their way out, and Lennier confirms that they are all dead. Delenn breaks down in Sheridan's arms.
Sometime later, the station is mostly back to normal. Delenn tries to convince Sheridan that if the other races have learned something from the experience and will use it for good in the future, then they will honor the memory of the Markab race. An ISN report says that the entire population on the Markab homeworld has been wiped out, and only a few Markabs on isolated colonies may have survived.
This has to be the single most tragic episode of all of the B5 series. The Markab race essentially doomed itself by hiding the plague from others until it was too late, based entirely on a religious belief and not scientific fact. If Markab scientists had been permitted to study the disease more extensively themselves and were allowed to work with scientists from other species, surely the cure that Franklin discovered would have been found - and before it was too late?
The situation as presented in the episode showed an extreme: it's unlikely that a whole species would follow a single religion with such devotion that they would all believe that only immoral Markabs would contract the plague, or that they would all obey their superiors and not discuss the plague with outsiders. If only a small fraction of Markabs had revealed their knowledge to alien scientists, then some work on the plague may have been done ahead of time, and it might have been stopped.
As it is, the Markabs were a significant species in the League of Non-Aligned Worlds, and we saw Markabs featured in "The Long Dark" and "Knives", for example. What will happen to the Markab homeworld (such as the resources on it) and their colonies?
We saw in the episode more signs of Franklin's overwork, although his compulsion is certainly understandable in this episode. Lazarenn chided him for using too many stims; we learned about the dangers of stim addiction last season in "The Quality of Mercy". Franklin was working too much in "In the Shadow of Z'ha'dum" as Ivanova noted, and we certainly got the impression that he was exhausted and depressed from his comments in "And Now for a Word". For how long can he keep up this work?
On another topic, where will Sheridan and Delenn's relationship go from here? Their conversation at the end of the episode seems to show them a bit more distanced from each other, but I think that's a pretty natural reaction after their premature revelations of their feelings earlier in the episode.
While Delenn was comforting the Markab child in the isolation section, she told a story from her own childhood. She became separated from her parents while in a big city and got lost. She found an old temple and decided to wait there. She fell asleep, and when she woke up she had a vision in which a male figure told her she would be safe - and then her parents found her. Who was this figure? Valen? Does Delenn think that this vision has marked her out as someone special or holy? She does seem to think she has a destiny vis a vis humans, and that's why she underwent the transformation in the chrysalis.
A smaller item from the episode: we learn that Keffer has been making as many trips into hyperspace as possible since he saw the shadow ship in "A Distant Star" He's trying to learn more about the ship. Sheridan finally realizes who that strange ship probably belonged to, and summarily orders Keffer's trips to stop. Needless to say, Keffer is not pleased.