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As the episode opens, the people on B5 are gleefully celebrating their victory in the Shadow war. But the sudden disappearance of the Shadows has left their minions in a state of confusion, as we will see throughout this episode.
First, on Earth, bigwigs in the Psi Corps brief Bester that recent off-world events have shaken President Clark. Gee, poor Clark's powerful backers have disappeared... but that means bad news for B5, as Clark orders a propaganda campaign to begin against B5. Travel from the Earth Alliance to B5 is now forbidden. Some Earth Alliance Starfuries are going to be posted a jump away from B5 to intercept ships heading for B5. Unbeknowst to those fighters, some Psi Corps Black Omega Starfuries will go there and destroy them - and then Clark can claim that B5 destroyed them. Of course, Bester has been helping B5 since last season in "Ship of Tears", so he heads for the station to let them know.
In no coincidence, Garibaldi receives some kind of message containing cryptic patterns; he deletes the message. Immediately afterward, he meets with Sheridan, Ivanova, and Franklin and resigns as head of security. The others are incredulous, but can't talk him out of it. He says he's tired of trying to save everyone all the time, and now that they've had a big victory, he wants to get out while he's ahead.
On Centauri Prime, Londo prepares to leave for B5, claiming he needs to get away for awhile so people can calm down after "losing" Narn. He cheerfully tells the overly effeminate minister (whom we saw all through Cartagia's reign) that he (the minister) has been named Regent until a new emperor is chosen. The look on the minister/Regent's face is priceless, and his first actions are to start improving the decor of the palace. Londo arrives on B5 with overflowing joy to be back, arriving just before Bester.
Bester is taken to meet with Sheridan and the command staff, Delenn, and Lyta. Lyta is there to make sure Bester doesn't try to take telepathic advantage of them, which Bester scoffs at, given Lyta's rating of P5. But then Lyta successfully blocks him, and he does take notice of her.
Bester tells them about Clark's plans for B5, but in return for the full information, he demands that Sheridan takes him to Z'ha'dum to look for technology left behind by the Shadows that might help heal his lover (from last season's "Ship of Tears"). Sheridan agrees reluctantly, and Bester tells them the full plans of Clark. Sheridan orders Ivanova to take care of Clark's plan while the others go to Z'ha'dum.
Ivanova takes a wing of Starfuries to the location of the Earth Alliance blockade, arriving just in time to wipe out the Black Omega Starfuries. The rescued Earth Alliance fighters are stunned to hear that their saviors came from B5.
When Sheridan, Bester, and Lyta arrive at Z'ha'dum on one of the White Star ships, they see numerous ships evacuating the planet. Lyta doesn't sense anything, but Sheridan orders a quick retreat from the planet. He's got good instincts, since the planet self-destructs in short order. Upon their return to B5, Bester spends a few minutes with the cryogenic unit containing his lover before heading back to Earth, telling her about his "ace in the hole".
Sheridan visits Lyta's quarters in a cold fury. He has concluded that a powerful telepath may have been able to trigger something on Z'ha'dum that led to its evacuation and destruction. Lyta agrees it's hypothetically possible. Sheridan explodes and declares that if such a command-level decision were made without consulting him again, he'd turn Lyta over to the Psi Corps for dissection. Lyta is completely cowed. I have to give Sheridan credit for having a lot of guts - he's just realized Lyta is much more powerful than she used to be, but he has no problem cutting her down to size. I suppose that's what having the moral authority of command will let you do, but just imagine what Lyta could potentially do to him.
At the end of the episode, Sheridan and Ivanova ponder where the Shadows minions went to after they left Z'ha'dum... and we switch to Centauri Prime, where the Regent wakes up from a nightmare. He looks under his nightclothes and finds a Keeper on his shoulder, like the one on Londo in the flash to the future last season in "War Without End, Part 2". Now we know where the Shadow's minions have gone.
This episode was not horrible exciting or suspenseful in itself, but it clearly set events rolling that will have long-term impacts this season and next season. Anyone who thought the Shadow war being over meant that there was nothing left to happen was seriously mistaken.
First, as I said, it's no coincidence that Garibaldi resigned after receiving his mysterious message, and no coincidence that said message arrived after Bester found out about the new plans regarding B5. Given that we know Garibaldi was in control of the Psi Corps (from the uniforms of the guards in his interrogation chamber in "Whatever Happened to Mr. Garibaldi?" and that we know the Psi Corps can manipulate people's minds and control them without their knowledge (season 2's "A Spider in the Web" and "Divided Loyalties", for example), it seems likely that Garibaldi is under Psi Corps control. Perhaps even Bester's direct control - is he Bester's "ace in the hole"? The next question is: why did Bester want Garibaldi to resign? Is he just trying to divide and conquer the B5 command staff? To what purpose, since he wants them to help his lover? We don't know what's going on here, but it's clearly going to have long-term effects.
Garibaldi then has to run the gauntlet of no one believing he's doing the right thing (and they might even be right!), which is not calculated to help his mood. There is a very nice scene, though, where G'Kar finds Garibaldi and thanks him for being a good enough friend that G'Kar went to search for him in "Whatever Happened to Mr. Garibaldi?" G'Kar's search ultimately pushed him into the events that led to him securing the freedom of Narn, so G'Kar is overflowing with gratitude. Garibaldi had been afraid G'Kar would be angry, since he ended up going through so much torture and even lost his eye. This is a great demonstration of how one's point of view can make you feel two difference ways about events.
The other big long-term effect of this episode is the infestation of Centauri Prime by the Shadows' allies. Morden warned Londo in "Into the Fire" that the Shadows had allies, but I don't think Londo had any idea what that might lead to. Given that Londo is under similar control by a Keeper 17 years later as the Regent is now, it seems safe to say that the events here are what ultimately lead to the decay and destruction seen on Centauri Prime in last season's "War Without End, Part 2". Londo was only doing what he thought he had to do in "Into the Fire", destroying the Shadow ships on Centauri Prime, but now he's doomed his world and himself. We are finding this out at the same time we see Londo so ebullient at returning to B5.
Sheridan and Bester's trip to Z'ha'dum was bound to happen sooner or later by someone - someone would be curious about what was left behind by the Shadows. Given the twisted nature of the Shadow technology we've seen, it seems like it's for the best that whatever was left behind on the planet was destroyed. Another question remains: what was left behind on the Vorlon homeworld?
I think Sheridan has missed another opportunity here with Lyta. He's just reasoned out that she's a much more powerful telepath than she was before, and he knows she has no love for the Psi Corps. Why doesn't he take her under his wing, and make her some kind of aide? Maybe that's not a proper Earth Force position, but they aren't part of Earth Alliance right now, anyway. Even though he's angry with Lyta at the moment, surely he realizes that she could be a very useful ally. Instead, he makes her feel like a disobedient child and does nothing to encourage her to help him out in the future. I suppose he figures she doesn't have anywhere else to go.
Lyta's situation is pretty bad. She no longer has the patronage of the Vorlons. How is she going to make a living? As Zack told her, many people are distrustful of her because of her connection to the Vorlons, so she has few friends. I would also think that her being a telepath would also make other humans keep their distance, since telepaths are ostracized on Earth.