Anna Sheridan, John Sheridan's lost wife, returns to the station, unexpectedly showing up at Sheridan's room, much to the shock and anxiety of Delenn. Anna attempts to get close to John, only to have him pull away. Anna explains that she will take any tests necessary and answer any questions to prove she is who she says she is. She says that she has come to explain to John what is really happening. She tells him he has to go with her to the Shadow homeworld, Z'ha'dum.
Meanwhile, G'Kar and Ivanova walk through a storage bay, where G'Kar explains that the devices around them were delivered by the Gaim ambassador, and that each of the weapons can deliver a blast of between five and six hundred megatons, and they are very difficult to detect. Ivanova plans to use them as mines to destroy Shadow vessels when they come out of hyperspace.
Sheridan has Anna checked over in medlab to make sure she is who she seems to be. Dr. Franklin states she appears to be his wife, but she has some epidermal scarring that he cannot explain. Sheridan tells him to keep checking her, as he has to know if it is really Anna.
In Sheridan's office, John confronts Delenn. He was led to believe, by Kosh and Delenn, that Anna had died on Z'ha'dum along with the rest of the crew of the Icarus. John demands to know why Delenn didn't tell him if there was even the slightest chance Anna was still alive. Delenn says that if she had, he would have gone to Z'ha'dum after Anna, and they couldn't allow that. John leaves the office, angered at not having had the choice of going after Anna and wondering if he can trust Delenn again. Delenn pleads after him to believe that no matter what, her love is real.
Vir finds Londo in the Zocalo drinking heavily. Londo explains that he has been promoted to the position of advisor to the Emperor in matters of planetary security. Londo clarifies that he's upset because the promotion means the Centauri want to put a leash on him so they know what he's doing at all times. He knows that if they see him doing anything suspicious, he will soon be killed. A man who identifies himself only as "a friend" approaches the table and tells Londo to leave the station at once if he values his life. Londo and Vir know that it was more than likely a friend of Morden's.
As Dr. Franklin searches for an explanation for the epidermal scarring, Anna tells Sheridan that the medical reports have confirmed that she is Anna. Sheridan wants to know why she picked now to come back. Anna cannot answer him until he comes back with her. Sheridan asks what will happen if he doesn't go, and Anna says she will leave without him, and he'll never know the truth. She promises no threats and no ultimatums--merely an opportunity to hear their side of the story. Sheridan still refuses until he gets some answers--he wants to know what happened to the Icarus and its crew when they landed there. Anna asks him if, when she tells him, he promises to go back with her, and Sheridan agrees.
Anna explains that Interplanetary Expeditions (IPX) said that one of their probes out on the Rim had found the ruins of an ancient civilization. Dr. Chang was putting together a follow-up expedition and he wanted her on his team. What he didn't tell the crew was where he really got the information.
A few years earlier, IPX had found an alien ship buried beneath the surface of Mars. As soon as it was exposed to daylight, an automatic beacon on board sent out a coded message. IPX knew whoever the ship belonged to would be coming in fast to pick it up, so they moved quickly. They analyzed the ship, took pieces of it for study later, and planted a homing device inside. Three days later another ship turned up, digging it out of the ground. When it left, IPX was able to track it through hyperspace to a world out on the Rim. Sheridan realizes this world was Z'ha'dum.
Chang was under strict orders from EarthForce New Technologies Division to keep the mission top secret. Upon landing, the Icarus' crew detected an energy source. The crew is ordered to investigate, the result being that they discover the Shadows.
Anna tells Sheridan that "Shadows" is not a descriptive name, nor their true name, which is very long and nearly unpronounceable. Anna says that there was an accident, the crew was killed, and the communication system was destroyed. They had no way to contact anyone else. She says that since the Shadows had just come out of hibernation, they made a deal with the crew: If the humans would stay silent, the Shadows would let them study their technology, which would solve nearly all of Earth's problems and let them leap forward 10,000 years. Anna says she didn't want Sheridan to think she was dead, but reminds Sheridan that he always said his first duty was to Earth. She says that Delenn, Kosh, and the others have misled him, and it's time to learn the truth. Sheridan agrees and embraces Anna, but while he does so, his gaze falls on Franklin's medical report on a table across the room.
Garibaldi enters Sheridan's office and asks if there's anything he can do to help. Sheridan tells him that he wants Garibaldi to begin logging the Minbari crew of the White Star into the security net. The White Star can orbit the station on autopilot. Garibaldi reluctantly agrees. Sheridan says he also has a few other things for him to do, and hands him a list. Garibaldi agrees to do it, but is more than surprised by what he sees.
As Sheridan prepares to embark, he packs his PPG and pulls out a second PPG, which he examines critically. In his reflection in the mirror, Ambassador Kosh appears and tells him that if he goes to Z'ha'dum, he will die. Sheridan records a time-delayed message to Delenn and goes aboard the White Star with Anna, and sets off for Z'ha'dum.
Once in orbit around Z'ha'dum, Sheridan and Anna take a shuttle down to the surface of the planet. Wearing oxygen masks, they make their way through the harsh atmosphere to the entrance of the main structure. The air inside is breathable, and Anna explains, for security reasons, the structure was moved underground many centuries ago. Before going further, Anna takes Sheridan's PPG before she will let him go further. She explains this part of the complex was designed specifically for them. She takes him down a corridor, and to a door. She knocks, and a voice inside tells her to enter. She does so, and inside are two humans. One is an older gentleman, Justin, and the other is a very familiar face: Morden.
On Babylon 5, Delenn plays Sheridan's time-delayed message: "Delenn, by the time you get this message, I will be at Z'ha'dum... with Anna. I can pretty much guess your reaction when you hear this, but I think it's the only way. When you and I were in the time rift with Babylon 4, for a moment, I jumped forward in time. We'd won the war, but Centauri Prime had been devastated. You said that this future couldn't be changed. You also told me, 'Do not go to Z'ha'dum. Do you understand? Do not go to Z'ha'dum!' I began to wonder... What if that future happened because I listened to your warning and didn't go to Z'ha'dum? What if... what if I could prevent the fall of Centauri Prime and end the Shadow War by going there? What I want... is to stay alive, to be with you. But you were right before. This is about more than what I want. So I'm going, even though I know it's almost certainly a trap."
Back on Z'ha'dum, Justin explains to Sheridan, "Back, a million years ago, there were forces prowling around the galaxy beyond anything that we could understand. And, like anything else, most of them outgrew this little corner of the universe, and headed off toward greener pastures. Now, two of them stayed behind, shepherds, you might call them. They wanted to look after the younger races, bring them around, help them evolve into something better." These two races are the Vorlons and what Sheridan calls the Shadows.
Justin likens the Vorlons to lords of order, while explaining that the Shadows believe that strength only comes through conflict. He admits that it is unfortunate that some races are lost along the way, but that cannot get in the way of a dream. The assistance of the Vorlons and Shadows was supposed to be equally balanced, but the Vorlons concluded that their way was the right way. According to Anna, they enlisted the support of the other worlds, like the Minbari. They even started interfering with the development of younger races.
On Babylon 5, Corwin reports to Ivanova that he is picking up a disturbance coming from all around them. Many Shadow ships appear outside, encircling the entire station. Ivanova orders a red alert, and all the fighters are scrambled. None of the Shadow vessels attack, but Ivanova still orders the fighters to launch, but not to approach until she authorizes it. As the fighters begin to mobilize around the Shadow vessels, Garibaldi among them, Ivanova tries to get through to Draal, but communications are being jammed. Ivanova knows the ships' appearance has something to do with Sheridan, but has no idea what it is, or why they are waiting.
On Z'ha'dum, Anna explains that the races must fight each other to grow and evolve. Justin explains that they cannot simply kill Sheridan as someone else would just take his place. Justin gives Sheridan a choice to willingly or forcibly join the Shadows. Sheridan asks if this is what the Shadows did to Anna, as he reaches for his second PPG hidden on his leg. Justin admits that Anna originally chose not to cooperate either. Sheridan asks if they had put Anna in a Shadow vessel, explaining how the station crew had recovered a ship full of people being prepared for that very use. Justin admits that Anna had been part of a ship but had been removed as soon as they realised who she was. However once someone has been inside a Shadow ship, one is never quite whole again. Viciously, Justin adds that Sheridan will do as he's told, as Shadows slowly enter the room. Sheridan draws the PPG and fires upon the Shadows.
On Babylon 5, G'Kar runs into Command and Control. Ivanova asks if they can get the bombs outside, but G'Kar says it would be too dangerous -- the blast would take out Babylon 5 as well. Ivanova is willing to risk it, and asks how many they have. G'Kar explains that's why he's there -- two of the devices are gone.
Sheridan makes his way to a balcony overlooking a Shadow city, with a black abyss directly beneath. Trapped, Sheridan is cornered by Anna trying to convince him to surrender. Sheridan quietly signals the orbiting White Star to crash into his location with the two armed thermal fusion weapons aboard. The White Star begins its descent.
Back in Delenn's quarters on the station, Sheridan's message concludes: "Finally, I heard what you said when I left. I want you to know, I love you Delenn. Goodbye." Delenn touches the screen, and as the message ends, she collapses against the wall, crying.
On Z'ha'dum, Sheridan can see the White Star on its way through the semi-transparent ceiling. Anna and several Shadows move in closer, as Sheridan turns away, staring into the abyss. Just before the White Star crashes through, Sheridan hears Kosh's voice telling him to jump, which he does. Anna is stunned, but has no time to further react as she looks up to see the White Star crash through the ceiling. Anna lets out a blood-curdling scream as white light engulfs the balcony along with a devastating explosion.
The Shadow vessels surrounding the station all vanish immediately. While Garibaldi watches, a shadow comes over his viewport. No one on the station understands the sudden departure, unless it is because they are no longer a threat, as G'Kar suggests. Ivanova believes she knows why, though. "He's gone."