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Each of the plots in this episode has its own revelation to contribute. The plots are intertwined in the episode, but they are distinct enough that I'm going to discuss them separately.
The plot that is most immediate for our main characters is Garibaldi's recovery from being shot in the back. Franklin has tried all the conventional treatments, but has come to realize that Garibaldi is not responding to any of them. He requests Sheridan's permission to use the alien healing device from season 1's "The Quality of Mercy". Sheridan agrees, and they ultimately end up sharing the burden of donating life energy to Garibaldi.
Garibaldi does awaken sometime after the treatment and is understandably upset when Ivanova tells him that his warning was not in time to save the President's life. He's also upset that Sinclair has been re-assigned - his paranoia is much more obvious than usual when Sheridan introduces himself, and Garibaldi says, "I don't know you!" Come on, Garibaldi has been in Earth Force for some time - being re-assigned is part of the job.
Garibaldi can't remember enough about the shooting to know who shot him, but he talks Talia into scanning him. Talia warns him that whatever she sees is not admissible in court, but he's willing to go through with it anyway. Luckily, when Talia "replays" his memory of the shooting, it makes him remember the details, too - including a convenient reflection of the face of the shooter, Garibaldi's aide.
Garibaldi and Sheridan waste no time setting up a situation to neutralize Garibaldi's aide safely. We see the loyalty many of Garibaldi's subordinates have for him as Lou Welch offers that Sheridan could "take a walk around the block" while he talks to Garibaldi's aide. Garibaldi insists on leaving medlab to interrogate his aide himself. His aide mostly scoffs at his questions, saying that the Homeguard is full of misfits, which implies a bigger organization was behind the President's assassination. Before Garibaldi leaves him, his aide makes the same farewell salute that Bester made before leaving in season 1's "Mind War".
The President contacts Sheridan and orders Garibaldi's aide and all evidence and records of the case be sent back to Earth for a full investigation. Sheridan doesn't like it, but he has no choice. After the prisoner's ship leaves, Ivanova tracks his progress and learns that he (and the records and evidence) were eventually transferred to a ship with an unknown registry and provenance - he's gone. This is very convenient, given how Earthgov was hotly denying any kind of assassination conspiracy.
The second plot involves G'Kar's return. At the end of last season in "Chrysalis", he had left B5 to search for information on the new power he believes must have destroyed the Narn outpost in Quadrant 37. In this episode, we initially see him in a Narn fighter, along with others, fleeing small, black, spider-like fighters that are similar to the larger Shadow ships seen previously. G'Kar is the only survivor.
When he returns to B5, G'Kar examines his Book of G'Quan, finding references to a great war 1000 years ago, with sketches of alien warships that look like the Shadow ships. He is convinced that this enemy has returned, and calls for a Advisory Council meeting to discuss it. The others are skeptical, but G'Kar says that they will have proof when a Narn ship arrives at the primary enemy world, Z'ha'dum, in 12 hours, takes images, and leaves immediately.
Morden had fortuitously just asked Londo to forward to him any information about the galactic rim, so Londo tells Morden about the Narn ship going to Z'ha'dum. It's no surprise to us that when the ship arrives, a waiting Shadow ship destroys it immediately.
G'Kar and the others on the Council are waiting together for news from the ship. Na'Toth says that the ship was destroyed by a malfunction after jumping. G'Kar dismisses this idea and immediately suspects that the ship was attacked. We see the connections coming together in his mind as he realizes that only the people on the Council knew about the ship, so if an ambush had been planned, one of them conveyed the information to plan it. He realizes that in many ways, his warning about the new/old power is too late - someone there already is working with them. I don't think that he has figured out who is working with them yet, but it won't take him too long.
This plot adds a new dimension to G'Kar. Previously we had seen him mostly as a bloodthirsty warmonger looking for revenge. But now he realizes that there may be more powerful races on the galactic stage, and the less powerful races will need to join together to oppose them. He even discusses this relatively amicably with Londo. Unfortunately, he may be unwittingly setting his planet up for retribution by Morden's associates, because they won't want the Narns messing up their plans, and so far the Narns are the only ones that seem to know about them.
The third main plot in the episode involves Delenn's transformation. While Lennier is away, she breaks out of her chrysalis and manages to put on a robe. When Lennier finds her, she is very weak and seems uncertain about what has happened to her. In desperation, Lennier calls Dr. Franklin to look at Delenn. She seems to be covered by some kind of cracked, gray scales, which break away when Franklin handles them. From what we see of Delenn later, these scales seem to be part of the transformation process, perhaps some of her old skin? When the scales break away, her new appearance is revealed.
Delenn chooses to reveal her new appearance at the end of the Advisory Council meeting where they find out the Narn ship is destroyed. When she removes her hood, we see that she still has a Minbari bone ridge around her head, but underneath that, she has long, human hair. We don't know whether her transformation is purely superficial, or whether she now has some human DNA and genetic features.
The other Council members are stunned, to say the least. Amusingly, Londo and G'Kar both have identical, jaw-dropping expressions. Sheridan seems pleased to see her, but he is not prejudiced by having known her before. Delenn announces that Sinclair is now on her world to foster understanding between Minbari and humans, and so she has transformed herself in order to provide a further bridge between Minbari and humans.
Delenn's transformation, which seems to have made her a combination of Minbari and human features, is a physical representation of the Minbari beliefs Lennier revealed in the last episode ("Points of Departure"): that Minbari souls are mixing with human souls. Delenn and presumably others among the Minbari seem to think that humans and Minbari are destined to mix and join, perhaps in order to save the future of both of their races. Although Delenn says her government approved her transformation, we have to wonder about this, given Hedronn's reaction to it in the previous episode. Perhaps she is simply saving face for them.
The final plot in the episode is the visit by John's sister, Elizabeth. They are happy to meet, and it's obvious that they used to be very close. We find out that their relationship has been very strained since the death of John's wife, Anna, two years ago. Anna was a scientist who had been a friend of Elizabeth's and presumably met John through her. John and Anna could only get together occasionally because of John's military schedule, but they seem to have been very close nonetheless.
John and Anna had planned to get together on their anniversary, but duties came up that caused John to cancel at the last minute. Anna signed up as the science officer on an exploration ship, and the ship exploded mysteriously. John has always blamed himself for canceling their meeting and "forcing" Anna to take the exploration trip. We see him get teary-eyed even two years later describing what happened.
Since Elizabeth and Anna were friends, John has been avoiding Elizabeth since Anna's death. Elizabeth keeps trying to get John to move on and release his guilt, but doesn't have any luck. Finally, she gives him part of a message that Anna sent her just before she left on the expedition. In it, Anna says that she had accepted the exploration assignment before John canceled their meeting, so she remarks that things worked out well. She is radiantly happy, and we can see how John can miss her. The message helps John realize that he wasn't to blame for Anna's death, and it also gives him a bit of a chance to say goodbye to her.
This plot gives another dimension to Sheridan also. We have seen him be an effective and decisive commander already, and we have seen the depth of his friendship with Ivanova. The backstory on his wife gives him a much softer side, and shows the depth of his feeling.
We can also note a connection between Anna Sheridan's exploration trip and the Narn ship in this episode. Both ships were going to check out planets on the galactic rim that had remains of ancient civilizations. Both ships were destroyed. Was Anna Sheridan's ship going to Z'ha'dhum?
This episode really sets the stage for events throughout the rest of the season. There's a new, powerful race that is taking more of a hand in events - Londo is aware of them and is working with them; G'Kar is aware of them, but can't get anyone else to believe him. From what we have seen of Delenn's and Lennier's actions, they are aware of them, but aren't doing anything about them at the moment. The humans are pretty much blissfully ignorant - but for how long? We don't know what the Vorlons know, but I did notice that Kosh was present at the Council meetings in this episode, which is unusual.
Earthgov has for the moment successfully blocked any substantive investigation into the allegedly conspiracy to assassinate the late President. The crew of B5 are knowledgeable about those events, but they don't really have anywhere to go with that information or any good way to investigate it. They had speculated that Psi Corps may have been involved - from Garibaldi's aide's salute and a previous scandal of the Corps supporting then-Vice President Clark - but they can't do anything about it.