Delenn discusses her upcoming judgment by the Grey Council with her assistant, Lennier. The Council is to decide if, given her recent transformation, she is still suitable to be a representative among them. While Delenn still maintains the same loyalty towards her people, the radical change in her genetic make-up has caused many of her fellow Minbari to doubt whether she is still one of them. Lennier supports her and assures her he will be there for her regardless of the outcome.
Ivanova informs Sheridan about unusual sightings of an unidentified ship, as well as regular flight ships disappearing from the radars near the areas where the sightings have occurred. The Squadron leaders are unavailable, so Sheridan decides to lead the squad himself, as it has been a long time since he's had the opportunity to fly. Somewhere far from the station, a Narn ship is destroyed by a large cruiser, and the escape-pod with the pilot is beamed aboard the cruiser.
Delenn is getting ready to travel to her meeting with the Grey Council, when Lennier appears and tells her he's going to take the trip with her. She tries to talk him out of it, warning him about the disfavor of the Council towards herself and anyone who will support her. Lennier is indifferent about the consequences, and determined to stay by her side throughout the whole ordeal. Ivanova calls Sheridan to notify him about General Hague arriving earlier than planned. She complains about being kept in the dark, as it is her jurisdiction as well, when a member of the Joint Chiefs visits the station. Sheridan tells her it's a personal issue, having nothing to do with an official visit, and orders her rather abruptly to leave the matter alone.
Garibaldi, Franklin and Ramirez, a fighter pilot, are having a drink in the Zocalo, arguing about the consequences of the Martian atmosphere on their favorite baseball teams. Franklin bets Ramirez 30 credits that the Dodgers will win the Earth World Series over the Mars team. Sheridan and his escort take off for what seems to be a routine investigation. Delenn and Lennier arrive at the constantly mobile Minbari cruiser that is the home of the Grey Council. Delenn must walk into the council chambers alone, to hear the verdict.
Just as Sheridan and his fighter Squadron prepare to leave the area, not having found anything suspicious or unusual, the unknown cruiser appears, firing directly at them. After the initial evasive maneuvers and an effort to fight back, all the fighters are destroyed except for the one handled by Ramirez. Sheridan is forced to launch his escape pod, a few seconds before his engines hit critical and explode. The cruiser beams his pod aboard as it did earlier with the Narn pilot. Ramirez checks the status of his damaged fighter. Communication is down, power supply is at 10% of its capacity, and the radiation leak from the fusion reactor has already reached terminal level. Ramirez has no chance of surviving. His only concern is to make it back to the station, so that the others will know what happened to the Captain. He redirects all available energy from life support to system controls, and so is able to open a jumpgate to Babylon 5.
Ivanova welcomes General Hague to the station, who is worried about Sheridan not being there, as it isn't his customary behavior to be late for meetings. Meanwhile, aboard the alien ship, Sheridan is incapacitated, wrapped in a cocoon, while being examined and tortured by surgical instruments. Delenn enters the Council chambers to find only Hedronn, who has come to announce her removal to her. Her transformation and companionship with the humans on Babylon 5, have made the Council believe they can no longer trust her. She is alien to them, and must be removed from their presence. Delenn is obviously hurt, as well as shocked, but she maintains her composure. She asks Hedronn for a hearing with the Council, concerning her position as Ambassador on Babylon 5.
Back on C&C, the jumpgate is activated and Ramirez's ship goes through. The life signs he is emitting are almost imperceptible. Ivanova requests an emergency medical team. On the alien ship, the surgical instruments stop examining Sheridan. He is released from his cocoon and given a weapon. A few seconds later a Drazi appears, wielding the same weapon, with an odd device attached to his head. He attacks Sheridan and they fight, with the Captain trying to talk to him and convince him to resist the urge for attack. Apparently the device on his head causes the urge for aggressiveness. The Drazi fails to resist it however, and soon after he is killed. His body vanishes, and a Narn appears with the same device on his head, and the same weapon. The Narn seems to be putting up more of a resistance to the device. Sheridan encourages him to keep resisting. The Narn begs him to kill him, so that he can be freed of his torture. Sheridan incapacitates him, but refuses to kill him.
Franklin does his best to save Ramirez, but it's too late for him. "Guess I won't collect the 30 credits", he tells the doctor before he passes away. Franklin is devastated. Ivanova comes down to Medlab and lets Garibaldi know what the data from the damaged Star Fury showed. The Captain has been taken prisoner by an unknown ship, with an unknown configuration, as well as destination. Delenn faces the Grey Council in its entirety, in her plea to remain as Ambassador on Babylon 5. She addresses them while yet her replacement is unknown to her:
Delenn while addressing the Grey Council at her hearing: I called many of you friends. Now you call me outcast. You know me. You know I believe in the task that is before us. The Great War that is coming. I have not turned my back on you. In trying to help, I have sacrificed all that I was and all that I am. We can no longer allow ourselves to be separated by names and borders. Our two sides must unite, or be destroyed. Do not make my sacrifice a vain one. Allow me to finish what I started. In the name of our friendship, and the future of our people, let me remain on Babylon 5.
At which point Neroon, a representative of the warrior cast, is revealed as her replacement. Delenn is outraged at what she sees as an injustice. The Council was supposed to have three representatives for each caste, maintaining equality among the people. Four representatives from the warrior caste give them a huge advantage in decision-making. Neroon and Delenn have a heated discussion over the subject:
Delenn: When Valen called the Nine together, he chose three from the Worker caste, three from the Religious caste and three from the Warrior caste. My replacement should've been from the Religious caste. Four from the Warrior caste gives them unprecedented power.
Neroon: Why not? It was the warrior caste who died in the war against the Earthers, the Warrior caste who have defended our world for centuries, while the Council floated among the stars, isolated from its own people.
Delenn: This is wrong.
Neroon: Is it? You say the prophecy says a great war is coming. Should not the Warrior caste lead against it?
Delenn: The Warrior caste cannot be allowed to set policy!
Neroon: Have you done any better? When I was inducted into this circle I was finally told the reason why we were ordered to surrender. I didn't know whether to laugh or weep! If we had been told the truth then, we never would have surrendered!
Delenn: You do not understand.
Neroon: I understand that before me is a creature I do not recognize. One foot in two worlds. You are an affront to the purity of our race! And your belief that you are satisfying prophecy is presumption of the highest order. And yet, it is true, that you are now the perfect liaison between us and the Earthers. You have no home with either of us. So please, act out your fantasy, be a go-between, return to Babylon 5. And stay there!
The lights are dimmed, the Council disappears and Delenn remains alone in the room.
The captured Narn on the alien ship awakes, and Sheridan tries to get some information from him. While the other prisoner was unconscious Sheridan removed the device from his head and dismantled it, so now they can talk freely. It seems that the ship's mission is to collect "specimens" so as to determine potential targets for invasion. By influencing the prisoners' brain they make them more aggressive and then observe their capacity for battle, as well as their survival rates. That way they can pick out the weaker races as targets of invasion. The Narn is desperate, and wants to give up, but Sheridan doesn't allow him to.
Lennier assures Delenn once more of his choice to remain with her, and they depart from the Minbari cruiser to Babylon 5. Back on the station, Ivanova and General Hague are still unable to pinpoint the location where the Captain has been taken, although they discern a general pattern in the alien ship's behavior. It jumps in and out of hyperspace picking up specimens.
Sheridan falls asleep, exhausted as he is from everything he has been through. His sleep is troubled by an enigmatic dream. He is standing in a darkened room, when Ivanova appears, a black raven on her right shoulder. "Shhh", she makes the gesture of silence, her index on her lips, and then asks him: "Do you know who I am"? Then he sees himself standing higher, as if on a bridge, dressed in a black uniform, and Garibaldi beside him, a white dove perched on his left shoulder. "The man in between is searching for you", Garibaldi tells him. Ivanova is standing behind him once again, this time dressed in a long, black dress, her head covered by a black veil. "You are the Hand", she says. Ambassador Kosh appears, surprising Sheridan, who asks him why he is there. "We were never away. For the first time, your mind is quiet enough to hear me". "Why am I here"? "You have always been here". Sheridan abruptly wakes up, troubled about the dream's significance. Invigorated by his rest, he figures out a plan to escape, by using the weapons as a lever to lift up the entrance door, and crawl out of it.
As Delenn returns to the station, she is notified of the Captain's abduction. When she receives the relevant data she fills the gaps with her own information. The race is already known to Minbari. The ship's mission, as Sheridan has already guessed, is to acquire samples of lifeforms for study. When in the past they had tried to do the same with the Minbari, they tracked them to their homeworld to make sure they didn't make the same mistake again. Delenn sends the coordinates of their homeworld to C&C. While Sheridan and the Narn prisoner are trying to escape, the rescue party from Babylon 5 arrives. Among them are Ambassador Delenn's ship, and the Agamemnon, Sheridan's old ship, who was called in to lend a hand. Sheridan and his Narn friend make it to an escape pod just in time, before the aliens space all the other prisoners. After having returned to the station, Sheridan checks with Franklin on the Narn's condition. He will be fine, but Ramirez is dead. "It's not fair", Sheridan says to the doctor. "Death never is", he replies. Ambassador Kosh is waiting for Sheridan outside Medlab. "You have always been here", he repeats.
A little later, in Sheridan's quarters, he and Hague have a private discussion. We learn that Sheridan is part of a covert military group with the purpose of exposing the conspiracy behind President Santiago's assassination, and reclaiming the government from Clarke and his associates. Sheridan has been waiting for six months to be debriefed. It seems that Clarke, with the help of some of the military and home Guard, and especially of the Psi Corps, has staged the assassination to look like an accident, managing to perform a "silent coup". But as Hague points out, "the trick is proving it". President Santiago arranged for Sheridan to be appointed CEO of Babylon 5 in case something happened to him, as his impressive military record makes him look like an obedient, easy to manipulate person. So for the time being, he is to operate discreetly, allowing Clarke to maintain the impression that he is on his side. That will give the others room to maneuver back home. Hague also presents Sheridan with the necessity of letting his officers in on this operation. It is a difficult decision, nevertheless one that needs to be made. Hague says goodbye to Sheridan and leaves.
Ivanova, Franklin and Garibaldi arrive in Sheridan's quarters. He explains to them what is at stake, and gives them the opportunity to leave the room before they get involved in anything they would perhaps need to report. All three of them choose to support him. As Ivanova says, "Wherever this goes, however it ends, we're with you".