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At the end of the first part, Sheridan had jumped into his future self, a captive of Emperor Mollari. We find out that this future is 17 years from the present, and Sheridan and Delenn managed to win the war against the Shadows. However, the remaining Shadow allies have decimated the Centauri homeworld, which Londo blames on Sheridan and Delenn.
Londo pronounces Sheridan's death sentence, and then has him thrown back in his cell. Delenn is brought to him there, and they share a joyful reunion, although in very different ways. Sheridan learns that they are married and they have a son named David. He tries to explain to Delenn that he's not supposed to be there, and Delenn remembers him telling her this story in the past. Delenn assures him that they have succeeded in everything they wanted to achieve, despite what appears to be a poor outcome for the Centauri - but at a "terrible, terrible price."
Londo sends for them, and he appears quite drunk. In a roundabout way, he explains that if he drinks just enough, the alien "keeper" attached to his shoulder will fall asleep and stop controlling him for a short time. He has purposely drunk the keeper to sleep so that he can arrange for their escape - the "last chance" for the Centauri. Sheridan and Delenn are confused, but follow his instructions to escape. As they do, Sheridan has a "time seizure" that will imminently send him to another time - Delenn realizes it and begs him to remember this message: Do not go to Z'ha'dum.
Meanwhile, Londo calls his "old friend" G'Kar into the throne room (G'Kar is missing an eye) for unfinished business. G'Kar begins strangling Londo to death, but Londo's keeper awakens and forces Londo to strangle G'Kar in return. They both die, and Vir enters the throne room to pick up the Emperor's sigil from Londo's body. (In "Point of No Return", Lady Morella prophesied that Vir would be Emperor.)
While this is going on on the "future", we see scenes in the "present" day of the others preparing Babylon 4 for the trip back in time. The device controlling the station's time traveling is cranky, and they go forward in time in fits and starts - just like was experienced in the first season in "Babylon Squared". During all of this, Sheridan appears intermittently as he drifts from the present time to his experiences 17 years in the future. Zathras jury-rigs a temporary fix to his time stabilizer, and Sheridan reappears and stays for long enough to help Sinclair make some adjustments to the station's power core. Then Sheridan disappears again.
During the problems with the time traveling, everyone experiences a "time flash" of events in their past or possible events in their future, what Sinclair and Garibaldi also experienced in "Babylon Squared". Delenn experiences a flash to the future: she's in Sheridan's quarters watching him sleep, when an unseen woman arrives and Delenn reacts with shock. After the time flash, Sinclair has aged significantly as a result of two exposures to the time traveling device - he was afraid it would happen, which is why he wanted Garibaldi kept away.
Sheridan continues to drift in time, disappearing and reappearing. At some point, Delenn switches places with him by giving him her time stabilizer and taking his place in the spacesuit. Sheridan is unconscious for a time from the stress of the time traveling, but is OK.
Besides working with the time traveling equipment, Zathras is also trying to fix Sheridan's time stabilizer. He is captured by Babylon 4 security, providing his presence in the events seen in "Babylon Squared" He explains to the first-season Sinclair and Garibaldi about Babylon 4 being needed in a war, but doesn't give away any crucial information. He fixes the time stabilizer, and when the spacesuited figure appears again, he gives it to them. Of course, at this point, it is Delenn. As in "Babylon Squared", Zathras is pinned down when everyone evacuates. The Sinclair from season one finally leaves him behind, and he is rescued by the present-day characters.
All of the equipment is finally set up and the Babylon 4 crew have been evacuated, so Sinclair tries to urge them all to go. Marcus calls him on his urgency - Marcus knows Sinclair is gearing up for some kind of sacrifice. Someone has to pilot Babylon 4 back in time, and Sinclair is ready to do it, even though he'll never be able to return. Marcus and Ivanova are aghast, but Sinclair has made peace with it. After all, he's known about it since he received the letter from Valen (in "War Without End, Part 1") - who is Sinclair. The others don't realize this until later, but the sharp viewer will catch it now.
Before they depart, Zathras speaks to Sinclair, Sheridan, and Delenn privately. He says they are all "the One": Sinclair is the One who was, Delenn is the One who is, and Sheridan is the One who will be. In a somewhat philosophical turn for Zathras, he compares this symmetry to the Minbari tendency to do things in threes. Zathras remains with Sinclair to go back in time.
As the others leave, Delenn leads the others to realizing that Sinclair is Valen, saying that the Minbari 1000 years ago never would have accepted Babylon 4 with a non-Minbari on board. We jump to watching Sinclair set up the triluminary device (like Delenn used for her transformation in season one in "Chrysalis") and go through a transformation, apparently into a complete Minbari. By the time he arrives at 1000 years in the past, the Minbari discover the station with Valen, Zathras, and two Vorlons to endorse it.
This episode does a spectacular job of tying up the questions presented by "Babylon Squared" as well as other big questions in the series. We had previously learned (in "Passing Through Gethsemane", I believe) that Valen was an Minbari not born of Minbari; this sounds pleasingly religiously cryptic, but in this case it is the literal truth. We also see now why Valen was such a wonderful prophet - he knew what events were going to happen, because they were history to the original Sinclair. Of course, this means that Sinclair as Valen couldn't prophesy beyond the events in this episode.
Sinclair becoming Valen also ties in nicely with Sinclair's Minbari attitude, commented on since the beginning of the series, such as in season one's "Legacies". It also explains why in the series premier "The Gathering" Kosh addressed Sinclair as "Entil'zha Valen". Was Kosh one of the two Vorlons on Babylon 4 at the end? I couldn't tell for sure.
Delenn ascribes Sinclair's transformation into Valen as the beginning of Minbari souls being born into human bodies. However, the basis behind this whole religious belief is lacking. After all, the Minbari deduced that Minbari souls were being born into humans after they captured and tested Sinclair during the Earth-Minbari war. Of course Sinclair has a Minbari soul, since he's Valen. Is there any other evidence of Minbari souls being born into humans? If not, I would say that besides Sinclair's major accomplishments 1000 years ago as Valen, another major accomplishment of his was to have stopped the Earth-Minbari war and brought humans and Minbari together to fight the present Shadow war.
The rest of the plot on Babylon 4 is pretty workmanlike, to make sure that all the proper connections are made to events we already know about. Sheridan's and Delenn's visions of the future are the other big highlight of this episode.
Sheridan's vision of the future tells us that the good guys are going to win the Shadow war, but leaves us with more mysterious questions: how did the Centauri get so screwed up, why does Londo blame them for it, and what is the "terrible, terrible price" that must be paid for the victory?
Before Londo released Sheridan and Delenn, he said it was his last chance; perhaps this was a chance to redeem himself that Lady Morella enumerated in "Point of No Return"? If so, how does Sheridan or Delenn qualify as the eye who cannot see, the one who is already dead, or his greatest fear? As we will learn in the next season, Sheridan would qualify as the one who is already dead - the "terrible, terrible price". At any rate, if Londo views this as his last chance for redemption, he may not really blame Sheridan for what happened to the Centauri - as Londo said, he had to put on a good show for his Keeper.
We get to see the "reality" (if you can call it that, since it's the "future") of Londo's death dream, revealed in the first season in "Midnight on the Firing Line. This is very satisfying, because otherwise how would we ever get to see something so far in the future compared to the other series events? But we have to wonder what happened to G'Kar's eye. I was pleased that Londo went out with another good line, "I am as tired of my life as you are."
Sheridan's jump into his future self also turns his relationship with Delenn on its head. We know they've been getting closer, but now we know that they will get married and even have a child. Amusingly, their first kiss comes now, which Delenn takes for granted, but is a new experience for Sheridan.
Delenn's brief look at her future reinforces her growing relationship with Sheridan, as she fondly watches him sleep. Who could walk in on her and surprise her so much?
These visions of the future bring up a question that Sheridan himself asks: if you know what's going to happen, can you do anything to change it? When Sheridan had jumped into the future, he was wondering if Delenn in that time could tell him anything to do to prevent the burning of Centauri Prime. Although Delenn denies it there, she doesn't hesitate to tell him later not to go to Z'ha'dum. Is that because he did go, and that caused bad things to happen? Or is that because he didn't go, but should have, and that's why bad things happened? The reality of the situation is that if Sheridan tried to change anything, he could potentially make things even worse. He got such a small glimpse of the future, how could he even know what to change?
What is the significance of Sinclair, Sheridan, and Delenn all being "the One"? Presumably it means that they are people that are in the right place at the right time to do huge things on the side of the Light. This echoes Mr. Sebastian's pronouncement at the end of season two's "Comes the Inquisitor". Delenn is the One making the decisions now - when will that switch to Sheridan? Perhaps it already is, as he takes over more and more fighting the war.