Garibaldi is eating his breakfast at mess hall, complaining to Sheridan and Ivanova about having the same breakfast every day for the past three years. As Ivanova and Sheridan tell him to "shut up and eat it", a special plate is delivered to Ivanova. It is a gift from Marcus because she helped him obtain an Identicard. The plate contains authentic eggs and bacon, which is practically impossible to get in space. Ivanova enjoys her breakfast as Garibaldi and Sheridan enviously watch her. Somewhere in the station, Marcus is tackling a bunch of thugs, trying to protect a woman from them, whom they are obviously chasing. It's a hard task as there are many of them, but Marcus pulls through, managing to neutralize all of them. The woman is unconscious but otherwise unharmed.
In the Zocalo, ISN reports the news concerning Clark's alleged illness that provided him with the alibi he needed to be absent when President Santiago's transport exploded. The matter has been fully revealed back on Earth, forcing Earth Gov to assume a defensive position. They are denying the allegations and using them, along with the appearance of the Shadows, as an argument for increasing the paranoia, both from within and from without. Their main defense is that a conspiracy has been engineered against them in order to destabilize Earth and make her more vulnerable to outside attacks. This kind of propaganda would allow them to proceed with extreme measures, with the excuse of protecting Earth at all costs.
In Medlab, the woman Marcus saved from the thugs is being examined by Dr. Franklin. Marcus explains to him that she is being chased down by "businessmen of a sort", who would very much wish to have her silenced. Garibaldi visits G'Kar in his cell, to check up on his condition. It seems G'Kar has taken up singing, to the other prisoners' dismay. Narn singing makes them believe G'Kar is being tortured. "You know, a true artist is never appreciated in his time", G'Kar tells Garibaldi. The quiet and isolation of the imprisonment have helped him focus on his thoughts and his inner world. He is writing his own manuscript, describing the events that led to the fall of the Narn homeworld, as well as the course that should be taken in order to assess and correct the mistakes of the past. Garibaldi is called to a 7R and leaves G'Kar with the promise of returning.
Garibaldi is explaining to the other members of the Council that the woman sitting with them, the one that Marcus saved, is in fact Dr Mary Kirkish, and he has been looking for her for quite a long time. She possesses valuable information, and that is why her life is in danger. Marcus used the resources of the Rangers to track her down and bring her to the station, at Garibaldi's request. Marcus brings Dr Kirkish in the room and she begins her story. She is an archaeologist conducting interplanetary missions to find evidence of life and technology on other worlds. Seven years ago, when she was stationed on Mars, her mission picked up a signal from something buried 300 ft. beneath the soil, in Syria Planum. Its formation and its depth indicated something artificial, not natural, that must have been there for at least a thousand years. The hard Martian winter slowed the digging process down and, after six months, only half of it was exposed. That half was enough to identify it as an alien vessel, terrifying and completely unknown. The vessel was the same as the one recently seen in the news.
The archaeological team immediately contacted Earth Central, excited about their new discovery. At first they didn't receive a reply. A worker who accidentally touched the alien ship was drained of his lifeforce within instants. A week later the scientists were ordered to pull back to their secondary base, and the digging stopped. Earth ships moved through the air as the scientists were locked in their bunkers, reduced to mere observers. After a while all movement and communication ceased. Another alien ship like the first one appeared in the sky, making a horrible noise. "A sound that just reaches right into your brain and rips it apart... The sound of something terrible being born". The second ship dug the first one out, the two of them disappearing in the sky shortly afterwards. The archaeologists were assigned to different expeditions, not allowed to talk about what they had witnessed. Garibaldi happened to be on Mars at the same time and, by chance, saw the ships leaving from a distance . He always wondered what had taken place on Syria Planum but, when he went to investigate the site a short while later, he didn't find much of anything, except a Psi Corps badge.
Now Dr Kirkish has been called in to a new expedition, this time on Ganymede. Another Shadow vessel has been discovered, and Clark's government wants to bring it to Earth in order to study it and use it against their enemies. Dr Kirkish risked her life in coming to Babylon 5, to make sure this kind of alien technology isn't put to use by Clark's government. Delenn asks Lennier to escort Dr Kirkish out, and fill her in on the arrangements that have been made for her. She is to be transferred to Minbar for her protection. Sheridan asks everyone but Delenn to leave the room. A decision must be made on how to deal with the issue.
The Nightwatch liaison enters Zack's office, reminding him there is another meeting. "Eternal vigilance is the price of freedom", he tells him. Before he leaves he makes a comment on the sense of omnipotence their position sometimes gives them. "You know, sometimes, watching them like this, without them even knowing we're here... Makes you feel a little like God, doesn't it? ". Zack remains silent. Sheridan contemplates his EarthForce badge, which he holds in his hand, when Delenn comes to pick him up. It is time to inform the others of their decision. As it is unacceptable for Clark to wield such power, the Shadow vessel must be destroyed before it gets to Earth. Delenn and Sheridan will use the White Star to go to the base at Ganymede, and destroy the vessel before Clark has a chance to seize it. It is practically a suicide mission, since when the White Star opens a jumpgate to Jupiter, it will be immediately detected and, except for the Shadow vessel, they will have to deal with EarthForce vessels as well. The decision has been made however. The White Star will not be captured regardless of the outcome of the mission. Sheridan leaves Susan and Garibaldi responsible for everything, informing them of the arrangements he has made in case they don't return. Any evidence leading back to Babylon 5 has been disposed of and a cover-up story has been prepared, which will present Sheridan's death as a combat accident.
As the White Star makes its way through hyperspace, back in the station the Nightwatch liaison puts forward a series of accusations during the meeting. According to him, several important people, including officers, Joint Chiefs of Staff and Senators, have betrayed Earth and the time to fight back has arrived. Nightwatch has been given full authorization to look into every aspect of every citizen's life, including their families, ideology and personal communications. Arrests will be made within the next two months. The increased state of insecurity and fear is being used as justification for the enforcement of Clark's totalitarian regime.
Lennier urges Sheridan to get some sleep, in order for him to be prepared for the confrontation ahead. Sheridan tries to make himself comfortable in the reclining Minbari bed, but fails miserably. Delenn comes to his rescue, explaining to him that meditation is required. Sheridan tells Delenn about the sound of rain, which always calmed him down and helped him sleep in times of stress. Once, the night before his final exams in the Academy, his father sprayed water with the garden hose above the roof, to create the illusion of rain. "He stood there making it rain until I fell asleep", he tells Delenn. He wishes it would rain now, so he could relax and sleep a little. Delenn says something in Minbari, and the ship begins to simulate the sound of rain. Sheridan sleeps, holding Delenn's hand.
Marcus reads his report from the Rangers to Ivanova, but she pays no attention, worried as she is about what will happen to the Captain. She blames Marcus for bringing this information to him, since he knew Sheridan would want to resolve the issue himself. "I'd rather assumed he would send me", Marcus retorts. After ranting for a while Ivanova admits she is just blaming him because there isn't anyone else left to blame. She is upset and confused by the whole situation, finding it difficult to accept the fact that they now have to stand against their own government.
Back in the White Star, Sheridan and Delenn are at the ship's command deck, after having rested. Dr Kirkish has provided them with the radio frequency of the military base in Ganymede, from which they are now receiving a signal. A person is preparing to enter the Shadow vessel to merge his or her brain with the ship, apparently operating as the vessel's central processing system. Once the merge has been realized, the ship will be fully functional. As the White Star increases speed, the merging is completed and the Shadow vessel breaks free, destroying the entire base and proving the folly of trying to harness alien technology without really understanding it. Sheridan fires at the Shadow vessel with the intent of drawing its attention. He plans to enter Jupiter's aerial mass, and wants the Shadow vessel to follow him. As the White Star plunges in, Sheridan hopes the enemy ship will not have regained enough of its strength yet to escape the planet's gravitational pull, and it will get sucked into its core. The White Star itself might not make it, but with the Shadow vessel following them, it is a risk they will have to take.
As the pressure and temperature increase, the White Star is in danger of being torn apart. Not a second too soon, they change their course from descent to ascent, managing to leave the Shadow vessel behind, destroyed by the planet's explosive atmosphere and extreme gravitation. Just as they emerge from this adventure, Sheridan's old ship, the Agamemnon, appears, notified of their presence by the attack on Ganymede. They think the White Star is responsible and order them to surrender and prepare to be boarded. Remaining in Jupiter's atmosphere, Sheridan refuses to return fire against his old ship, but the situation is getting more dangerous by the minute. Delenn has the idea to activate a jumpgate inside the atmosphere. Lennier protests that it will cause an explosion, due to the planet's high percentage of hydrogen. Sheridan replies that if they try to reach the edge of the planet's atmosphere, the distance should minimize the eruption. Signaling to the Agamemnon that they wish to surrender but need space to change their ship's course, they gain some room to maneuver and the White Star makes the jump as planned. It emerges on the other side undamaged.
Back at the station, Ivanova, Garibaldi and Sheridan are watching the ISN news bulletin. The report confirms the presence of an unidentified ship that led an attack on Ganymede and was then pursued by the Agamemnon, and was finally destroyed by it. The story is being distorted to present the White Star as the ones who attacked Earth rather than those who saved it. Clark is taking advantage of yet another incident to justify his measures of increased security. "You know what they say: No good deed goes unpunished", Garibaldi tells Sheridan.
In Zack's office, the Nightwatch liaison observes that even if Sheridan was supposedly in his quarters for two days, his personal computer panel hasn't been accessed and the security records have been falsified to cover his absence. That means Garibaldi is helping with the cover-up. The liaison asks Zack to put his duty before his friendship, and use his personal relationship with Garibaldi to get information about the secret conspiracy going on in Babylon 5. Zack refuses, and the liaison pressures him. When he leaves, Zack looks at the Nightwatch armband on his uniform, with what seems as an inclination to take it off.
Marcus pays Ivanova an unexpected visit in her quarters, holding an organizational chart of the station based on the Ottoman empire model. As she has previously expressed concerns about where he fits in the hierarchy, he chose this colorful manner of displaying his position to her. "It gets a little confusing around this bit here, but one has to start somewhere", he tells her. Ivanova laughs, and Marcus admits that was more or less his initial intention. Just before he leaves, Sheridan calls Ivanova in her ComLink, asking her to turn on ISN. As she and Marcus watch the news, they learn that Clark has declared martial law throughout Earth Central, for reasons of planetary security.