Ambassador Mollari is queuing at the entrance of Babylon 5, complaining to another passenger about the delays and inefficiency of the new Narn Security recruits. When his turn arrives, an excruciatingly polite Narn, who had overheard his ranting, pretends not to be able to read his authorization, sending him back to further waiting. In space, General Hague's ship, the Alexander, is under attack by another Earth vessel, the Clarkstown. Inside the Alexander's command deck, Major Ryan and Officer Trainor are discussing their situation. They desperately need to jump to hyperspace, but they cannot leave their fighters stranded and Major Ryan does not want to open fire directly to their vulnerable pursuer. Trainor insists that they have no choice and Major Ryan gives the order. The Clarkstown is destroyed. As they load the fighters and prepare to jump, Major Ryan talks about how the captain of the Clarkstown and Gen. Hague studied together at the military academy and how it will now be his duty to tell both their widows about their husbands' deaths. Officer Trainor asks for the jumpgate coordinates. Major Ryan says that there is only one place safe for them: Babylon 5.
In Sheridan's office, Sheridan, Ivanova and Garibaldi discuss the impending arrival of the Alexander. Sheridan wants Garibaldi to put a cut-off switch in the Com system that leaves only a private channel and the ISN feed open, to prevent someone from informing Earth as soon as the Alexander passes through the jumpgate. They all know that their cover will be blown then. At the docks, Lennier, Delenn and Dr. Franklin attend to an injured Minbari Ranger who is bringing vital information from a mission among the Non-Aligned worlds. They need to bring him to Medlab without alerting Security. G'Kar appears then and offers to carry him through customs, guaranteeing the discretion of his people within Security.
ISN broadcasts the news that the Mars Provisional Government will not implement Martial Law in their territory, thus openly defying President Clark's order. Earth's reaction to this defiance will not take long. Sheridan and Ivanova are poised in the C&C bridge waiting for the Alexander. As soon as the ship jumps through, Sheridan gives the order to Garibaldi to cut off the Coms and addresses the C&C personnel, telling them that the crew of the Alexander are not their enemy but their comrades and that it is his intention to give them humanitarian aid under his own full and personal responsibility. If anyone has a problem with this order, they should leave C&C now. They all choose to stay.
Back in Medlab, the injured Ranger reports to Delenn that many among the Non-Aligned worlds are falling under the Shadows' influence, some out of fear of the Centauri's new expansionist policy, some out of greed, and are now going to war against their neighbours. It is obvious that the Shadows have exploited Centauri Prime's nationalistic ambitions, as well as their traditional imperialism, to create instability in the area around their space. The smaller worlds around Centauri Prime who had been under Centauri rule centuries before, are driven by their awareness of their military and technological inferiority to expand themselves and form strong alliances. The Shadows are taking advantage of the general mayhem to impose their dominion in the area and create a distraction to keep their enemies occupied, using everyone else as pawns in their own elaborate chess game. The Minbari Grey Council has been informed of this, but they have chosen not to intervene, since the problems of others are not their concern. Both Lennier and Delenn are distressed after hearing this.
Major Ryan arrives in Babylon 5 and informs Sheridan, Ivanova and Garibaldi that Gen. Hague was killed in the battle with the Clarkstown and that he is trying to keep the crew together. Back on Earth, most of the people have accepted the new regime, since on the surface life looks much more peaceful than before. Clark has people in most of the key places and dissenters are arrested immediately and charged with treason. ISN is not reporting much of what is really happening because they fear that they will be shut down otherwise. The only hope now lies in the colonies. If other worlds follow Mars' example and refuse to cooperate with President Clark, there's still is a chance. As they are discussing, the Alexander contacts Maj. Ryan to inform him that EarthForce is now bombing Mars. Images show the new model fighters, able to maneuver in atmospheric environments, bombing civilian targets on Mars.
Delenn prepares to leave for a meeting with the Grey Council concerning their attitude. An Earth destroyer, the Churchill, under the command of Captain Hiroshi, arrives to join forces with Babylon 5 and the Alexander. Hiroshi also brings important news from EarthForce command. On the screens out in the station ISN is reporting a mild version of the Mars bombings when one of the reporters interrupts to announce that President Clark's forces are finally moving in on the ISN broadcast center. Before they are shut down, the reporter announces the previously undisclosed news that Orion 7 and Proxima 3 have broken away from the Earth Alliance in protest over the bombing of Mars and will remain independent until President Clark is impeached. Further revelations are interrupted by explosions and the ISN feed is cut off, just as Clark's forces invade the studio.
Capt. Hiroshi informs Sheridan and the others of the situation in Orion 7 and that President Clark is now sending troops to all major colonies that might follow the example of Mars, Orion 7 and Proxima 3. Clark also knows that the Alexander is in Babylon 5 space, and is sending two ships over, the Agrippa and the Roanoke. They are on their way with heavy reinforcements, and their mission is not only to destroy the Alexander, but to seize command of Babylon 5 and to arrest its command staff. Maj. Ryan offers to leave and give Sheridan a chance to negotiate, but Sheridan knows that the moment to stand up to Clark has finally arrived. Maj. Ryan and Capt. Hiroshi leave to prepare their ships for battle. Sheridan faces his people: Ivanova, Garibaldi, Dr. Franklin, and asks them for their vote on how to proceed: Surrender or Fight. One by one they all choose to fight. Prepping for battle, Sheridan orders Garibaldi to get all security teams, including the Narn ones, ready for boarding parties. All fighter squadrons should be ready and Medlab should free as much place as possible for incoming wounded soldiers. He will also need Draal's holographic system on Epsilon 3 to make an announcement.
Inside a Minbari cruiser, Delenn demands access to the Grey Council. When one underling tries to stop her, she reminds him that she was a former member and the one chosen by Dukhat himself to replace him. She held him when he died and now she will speak her mind to her former colleagues by force, if necessary. In the council chamber, Delenn reminds them of the thousand years endured preparing for the coming Shadow War, and severely reproaches them because now that the moment has arrived, they have ceased to believe in Valen's prophecy and have chosen the path of selfishness. This is the moment to fulfill another prophecy and break the now useless council and, if the Warrior cast does not wish to fight, the Religious and Worker casts, who control two thirds of their forces, should follow her to battle. In the pinnacle of her rage, she breaks the ceremonial staff of the Council leader in two, destroying the symbol of its unity, as that unity is now only superficial. Peace has turned to cowardice and self-interest. It is time to cast away the symbols of the past, and step towards the future in battle. As she leaves the room, five grey-clad figures, the representatives of the Religious and Worker casts follow her, leaving the four representatives of the Warrior cast alone.
Sheridan is making a last com call to his father on Earth. The former diplomat has guessed the reason for the call and tells his son that whatever decision he makes, his family will be behind him and that he should not worry for their safety. He reminds Sheridan of the lesson he taught him as a child: Never start a fight, but always finish it. With these words of encouragement, Sheridan returns to C&C and makes a station-wide announcement using Draal's holographic system, explaining about the impending attack and how President Clark had violated the Earth Alliance constitution with his coup on Earth and the attacks on Mars. He, as Commanding Officer and Military Governor of Babylon 5, has decided to follow the example of Orion 7 and Proxima 3 and declare the independence of Babylon 5 until President Clark is removed from office. He will grant free passage back to Earth to anyone who wishes it after the fighting is over, but now, all civilian population should remain in their quarters for their own safety. After the message, he asks anyone in C&C if they wish to leave before they violate regulation, and at least one person does so, but the rest stay. Sheridan also decides not to ask Graal for further military help from Epsilon 3 at that point, since he wishes to keep that asset secret for as long as possible. It will come in handy in the war with the Shadows, where Babylon 5 will need all the surprise elements it can get. Ivanova asks Sheridan command of the Starfury squadron, pointing out that at least one of them should be out there in the front lines with the soldiers that are being asked to fight against their own people. As much as Sheridan wants to protect Ivanova, he cannot deny the logic and fairness of that request. Babylon 5's Starfury squadrons are launched.
The jumpgate activates and destroyers Agrippa and Roanoke arrive, escorted by smaller fighting vessels. Captain Smith orders Babylon 5 and the "renegade" ships Alexander and Churchill to surrender. Both the Alexander and Churchill launch their fighters. Sheridan responds to the message trying to convince Capt. Smith that the orders they are following are illegal and should not be executed, but they break contact and Sheridan activates Babylon 5's defense grid. The enemy fighters initiate the attack. Ivanova takes point on her squadron and spears the attack on the enemy destroyers. Maj. Ryan follows with the Alexander, his reluctance to fight back gone. Breaching pods reach Babylon 5 and Garibaldi rallies his troops to stop the invaders. An attacking Starfury explodes right in front of C&C, but damage is minimal. Sheridan redirects the station firing to the Roanoke. The Churchill is now on fire and it is too late for Capt. Hiroshi and her crew to reach the escape pods. In an act of self-sacrifice, she rams the Roanoke before exploding. Ivanova's fighter collides with another Starfury and Sheridan orders her to eject before it explodes against the hull of the Agrippa. There is fighting in the station corridors and the Alexander concentrates its fire on the Agrippa, while Sheridan contacts the now critically damaged Roanoke and guarantees the safety of their crew if they surrender. It is however too late and the Roanoke explodes. The attackers stop firing.
Damage reports indicate there is damage in all sectors and fighting still goes on in Brown sector. Babylon 5's hull integrity is not good and will not withstand many more attacks. At that moment, the jumpgate activates and two more destroyers arrive to reinforce the attackers. The new arrival, Captain Drake, orders Babylon 5 to surrender and prepare to be boarded. Sheridan knows that the station cannot fight off two additional destroyers. Four jump points are forming on top of the station and Sheridan's despair turns to relief when three Minbari cruisers and a White Star, commanded by Delenn, jump out. Delenn immediately initiates dialogue with the attackers:
Delenn: This is Ambassador Delenn of the Minbari. Babylon 5 is under our protection. Withdraw or be destroyed. Capt. Drake: Negative. We have authority here. Do not force us to engage your ship. Delenn: Why not? Only one human captain has ever survived battle with a Minbari fleet. He is behind me. You are in front of me. If you value your lives, be somewhere else.
Seeing the point of Delenn's argument, the attackers withdraw and Sheridan orders all fighters to return to base. This battle has been won, but many are wounded or dead inside and outside the station. Garibaldi and Ivanova are safe but injured and the station has lost too many Starfuries. Maj. Ryan proposes to Sheridan to divide the Churchill's surviving Starfuries among them. He will leave Babylon 5 space as soon as his repairs are finished, so that President Clark's forces do not have a single target to focus upon. He also needs to contact other Earth ships that were friendly to Gen. Hague to try to build a rebel armada. As they leave, Maj. Ryan remarks that Sheridan is not wearing the jacket of his uniform. Sheridan replies that he cannot wear an EarthForce uniform with a clear conscience after that day. He will put it back again when the battles are over.
The station restarts its normal operations slowly, mainly shipping out people who wish to leave and those who need to be gotten rid off, like the Nightwatch. Not all of them are accounted for, though. Delenn arrives and she and Sheridan share a private moment. Sheridan confesses that the moment he saw her face on the screens was the finest of his life. Ivanova, Dr. Franklin and Garibaldi join them and escort them to the Zocalo, where the assembled population of Babylon 5 gives them a round of applause. Behind them, a half torn propaganda poster reads: "Traitors can't hide".