Captain John Sheridan is aboard his commanding ship, the Agamemnon, when he receives a gold channel transmission from General Hague. During the course of the discussion he is informed that a renegade Minbari warship, the Trigati, is approaching Babylon 5 with hostile intentions. He is to take care of the situation directly from Babylon 5, by assuming general command of the station.
In the meantime, Susan Ivanova is walking around the station, trying to appease the ambassadors and diplomatic attaches making her life difficult. Security Chief Michael Garibaldi is still in the Medlab in critical condition, after the attempt on his life when he uncovered the conspiracy to murder the late President Santiago. Ambassador Delenn on the other hand is undergoing a process of transformation in her quarters, and is therefore confined in a human-sized cocoon. Lennier watches over her and performs the necessary daily rituals. Ivanova receives herself a transmission from General Hague, informing her that Sinclair will not be returning to the station, as he has been appointed as Earth's first ambassador on Minbar, and that John Sheridan will be taking his place instead. Ivanova is acquainted with him from having served alongside him in the Earth-Minbari war. She expresses her concerns to the General, since Sheridan is a known and feared Minbari opponent and the destroyer of one of their best ships during the war, the Black Star.
A member of the Grey Council , Hedronn, visits Delenn's quarters and expresses his disagreement on her decision to undergo the transformation. "Now we are on the path", he says and leaves the room.
Sheridan arrives at the station earlier than expected. Ivanova meets up with him and gives him a quick tour of the station. It's the first time we learn about Sheridan's love for gardens, fruit, and in particular oranges. He is informed about Garibaldi's condition, about Ambassador G'Kar having mysteriously vanished and Delenn being in a cocoon. Their next stop is Sheridan's private quarters, were he has a heartfelt, honest discussion with Ivanova about his being chosen as CEO for the station, Santiago's assassination and the problems that may arise from his history in the war.
The commander of the Trigati, Kalain, arrives at the station incognito. He has a confrontation with Hedronn, and it is apparent from his opinions that he believes the choice for the new CEO to be a provocation for the Minbari. The internal conflicts between the castes in Minbar are also apparent, as the warrior caste believes the surrender was treason, and that Earth is still their enemy.
Ivanova drops by Medlab to have a talk with Dr. Franklin about Garibaldi's condition. He tells her there's no definitive way to predict how his situation will turn out. Sheridan and Ivanova then visit Command and Control, where Sheridan introduces himself to the crew and begins to give them his good-luck speech. They are interrupted by an emergency transmission, concerning new important information about the Trigati. Ivanova and Sheridan have a private meeting with Hedronn, who tells them everything about Kalain and his intention to cause trouble in the station. Sheridan and he get into a strong disagreement, which ends up in Hedronn expressing his dislike for Sheridan and leaving the room. "If there is a doom on this station, it is because you brought it here", he says.
Ivanova asks Sheridan about how he managed to bring down the Black Star, and he explains to her how he mined the nearby asteroid field to make sure the fusion bomb targeting the ship exploded. When it finally did it took the Black Star and two other ships down.
Kalain neutralizes a Babylon 5 guard and reaches Delenn's quarters, where he threatens Lennier to kill her. He doesn't act upon his threat however, and soon after Security apprehends him and confines him in lockup. Sheridan and Ivanova try to interrogate him but their efforts prove to be unsuccessful. Sheridan suspects there is a reason why he didn't kill Delenn, and tries to find out what that is.
Outside the interrogation room Lennier meets up with the two, and asks for a private audience with them. During the course of that discussion he reveals to them the true reason behind the Minbari surrender, and the events that are hidden behind it. During the Battle of the Line the Grey Council picked one human pilot randomly, for interrogation before the final strike. That pilot was Jeffrey Sinclair. While interrogating him the council discovered the solution to one of their long-term problems, that of reincarnation. The Minbari race believes that all the great souls are re-born into the next generation, but lately they had observed that fewer and fewer great souls were among them. Those souls were migrating into the human race, residing in human bodies. So in order for those souls and the collective future of their race to be saved, the Minbari surrendered instead of destroying the humans. That secret was considered dangerous to the stability of the social structure in Minbar, so it was never revealed to the Warrior caste. Warriors still don't understand nor approve of the surrender.
The emergency alarm sounds again, when the Trigate opens up a jumpgate and finds itself directly opposite the station. The ship's commander makes contact with Sheridan and refuses his plead to resolve the situation peacefully. "All that remains now is honor and death", she says and launches her fighters towards Babylon 5. Sheridan suddenly understands the situation. He sends word to Security and is informed that Kalain has committed suicide. The Trigati's intention is to create a situation where Earth will seem to have initiated military conflict, so that the Earth-Minbari war will start allover again. Sheridan orders the station fighters to remain in their positions, and notifies an official Minbari cruiser to come for the Trigate. The cruiser asks the Trigate to stand down and prepare to be boarded, but in response the renegades blow up their ship and commit heroic suicide.
A little afterwards Sheridan tells Ivanova he is having second thoughts about whether accepting the position in B5 was a selfish decision on his part. Perhaps the mistrust Minbari people have for him will prove an obstacle in running the station. Ivanova tells him to stop worrying so much, and to give himself the benefit of a doubt. Things might have turned out either way, regardless of who is CEO.
Lennier talks to Delenn, telling her he did what he was supposed to do, and revealed the secret to the commander. "I only wish I could've told them the rest", he says to her. Ivanova, Franklin and a pilot are having a drink wondering where Sheridan is. He is alone in C&C, finishing his good-luck speech, while the room is completely empty of personnel.