The alliance fleet is in hyperspace. Aboard a Minbari heavy cruiser, Marcus keeps watch over Ivanova. Delenn walks in, and tells him the transport to take Ivanova back to Babylon 5 has arrived. Marcus argues that she would want to be at the battle, and since she is dying there is nothing else to do for her. Delenn disagrees: they can make Ivanova comfortable in her last hours, and see to her needs, but not in the fleet. Marcus holds Ivanova's hand in his, and leaves without a word. Delenn also leaves, as two Minbari prepare to take Ivanova away.
At the Mars Resistance HQ, final preparations are underway. Number One arrives with an Earth Force officer, who will help smuggle the frozen telepaths onto the destroyers orbiting Mars. It will be tricky, but she'll try to make it work. Meanwhile, Garibaldi leads a small team scouting a supply base on the surface. They are two hours away. They begin to approach as shuttles leave the base to supply dozens of Earth Alliance Destroyers.
At a bunker on the perimeter of the base, an Earth Force officer asks for a status report. With Sheridan's imminent attack, they expect the Mars Resistance to take advantage of the confusion and attack. As the officer attempts to contact another station, an NCO pulls out a breather mask. The officer is getting no reponse. "What is wrong with Bravo?" he asks. The NCO puts the breather mask on, pulls out a gun, and answers: "Same thing that is wrong here." At that moment, the door to the bunker opens; with the atmosphere thinning, the attacking forces easily overpower the Earth Force personnel. The attacking forces include Number One, Garibaldi, Franklin and Lyta. The NCO indicates there was no opportunity to warn the base: the Resistance now controls the perimeter. Franklin puts a device on Lyta's head and starts working on it.
Aboard the Agamemnon, Sheridan gives the attack fleet their final instructions. In order to attack Earth, they must take out the bases on Mars first; otherwise, they would expose their flank and end up fighting on two fronts. The Earth Destroyers and White Stars will lead the assault, and the League ships are to provide support and establish a perimeter, but they are not to engage unless fired upon first.
Aboard the Apollo, leading the Earth Force destroyer group, General Lefcourt is in command. He has been called to replace the Apollo's captain because Lefcourt is a soldier of the old school: he does not take arms against his own government, no matter how justified he may feel. And because he taught Sheridan at the Academy, and knows how Sheridan thinks. Now he has to kill him, and everyone around him. "It's a terrible day," he tells the Captain. "I wish to hell I had never lived to see it."
Lefcourt is informed the hyperspace probes have picked up something, but decides to wait in normal space for Sheridan. No engagement in hyperspace has ever been anything but a disaster for both sides, and Sheridan will come out sooner or later.
On the Mars surface, Franklin finishes adjusting the implants on Lyta's head. She has to go outside to make contact; it will be really difficult because of the distance, she says. She leaves the bunker, and Garibaldi sends a final message to the fleet. Everything is ready.
Aboard a White Star, Marcus seems thoughtful. "You are thinking about Ivanova again." says Lennier. Marcus is indeed thinking about her, and how she is probably better off on Babylon 5, where there may be something they can do for her. Lennier advises him not to get his hopes up, but Marcus ignores him. Marcus has called Dr. Hobbs on Babylon 5. In all this time, he reasons, they must have come up with something to deal with near death conditions. "No." replies Lennier. "There is nothing usable on Babylon 5." Marcus asks what he means, but before Lennier can clarify, Garibaldi's message comes through.
In the bunker, Garibaldi tells everyone to get ready. He's given the fleet information accurate to within a few feet, which will enable the White Stars to jump from hyperspace inside the atmosphere. A White Star jumps in and starts attacking the base, helped by the Resistance which is using the perimeter weapons.
Gen. Lefcourt is informed that the Resistance has attacked four bases on Mars, and Sheridan's fleet is attacking a fifth. But Lefcourt does not want to be planetbound, unable to maneuver in the gravity well, and orders the fleet to stay in formation. He is curious, though. Sheridan wouldn't go on the offensive without an ace in the hole. What is it?
Meanwhile, Lyta starts contacting the frozen telepaths, now aboard the Earth destroyers. As Franklin explains, they are aboard 30 of the destroyers. They will awaken, merge with the computer systems and render the destroyers useless. They are being used as weapons, he admits, but they are weapons. He cannot remove the implants without the resources of Earth; if the Alliance doesn't win, the telepaths are dead anyway. And each destroyer has 1000 people on board. If they do not have to destroy the ships, they are risking thirty lives to save thirty thousand.
Aboard the destroyers, the telepaths awake slowly, as Lyta concentrates.
Sheridan's fleet jumps into normal space close to Mars, as Lefcourt expected. But before he can give any orders, the Apollo's systems begin to fail. Almost all of the destroyers report similar problems. In fact, all but 10 of the destroyers are out of commission. Sheridan orders a White Star squadron to open fire on them, targetting engines and weapons. Disable them, don't destroy them, he instructs. The squadron quickly accomplishes this.
Aboard the Apollo, a security detail finds the shadow-modified telepath and opens fire. Meanwhile, Sheridan is ready to proceed. Human and Minbari forces are to jump to Earth, while the rest of the League ships stay behind to keep an eye on the disabled destroyers. Marcus rejoins the fleet, but leaves Lennier in command as he goes to his quarters. He orders a search of Babylon 5 records relating to death, terminal illness, and extreme measures.
Marcus soon receives the results, and finds a reference to the alien healing device ("The Quality of Mercy.") He orders a shuttle to be made ready.
Aboard the Apollo, they have figured out the problem and eliminated the telepath, but most systems are still down; they have no engines, and no communications with the other ships, so they cannot let them know what they found out. Gen. Lefcourt angrily orders engineering to get the ship under control ASAP.
Lennier arrives at Delenn's ship. He has been tricked by Marcus into leaving Marcus' White Star. Marcus breaks formation and leaves. Delenn contacts Sheridan to let him know. They figure he is on route to Babylon 5, but they cannot contact the station: as soon as they got inside Mars orbit they hit the jammers. They are too close to turn back, and there is nothing to do but continue ahead.
The fleet jumps to normal space, and Sheridan talks to the people of Earth. He encourages those in the government who were afraid to speak up to help place President Clark under arrest, to disband Nightwatch, and to return the government to the hands of the people. As he does so, Clark writes in his office, the planetary defense grid comes online, and a group of armed security officers escort a woman down a hallway.
Sheridan continues: "This is not the voice of treason. These are your sons, your daughters, whose loyalties have never wavered; whose belief in this Alliance has forced us to take extraordinary means. For justice, for peace, for the future... we have come home."
President Clark hears people outside his office, and he types a final command for the defense grid. He takes a gun, and shoots himself in the head. The woman and the security detail break into the office to find Clark dead and a note on his desk. The note contains the phrase "The ascension of the ordinary man" over and over, with certain letters circled. The letters spell out "Scorched Earth."
As the fleet continues its attack on the defense platforms, the woman, who is Senator Crosby, contacts Sheridan and tells him of the death of Clark and his message. He has ordered the defense grid to fire on Earth, and they cannot override the command. In ten minutes, it will fire and level 40% of the surface.
"Delenn, we need you," says Sheridan. "We are there," she replies. The combined human and Minbari forces attack the defense platforms, destroying them one by one as Minbari and human pilots give their lives in the process.
The Agamemnon is hit several times by missiles, as the race to destroy the platforms continues. The Agamemnon is hit again, and is now heavily damaged and unable to fire. The nearest platform is about to fire, and no other ship is in range. Sheridan gives the order to ram the platform in a suicide run.
But before they can hit the platform, the Apollo comes out of hyperspace. "We have monitored the situation. Hold on to your hats," says Gen. Lefcourt as he fires and destroys the last platform. The Agamemnon emerges from the fireball, still in one piece.
"You'll have to stand before a board of inquiry on this one, Sheridan," says Lefcourt. "Still, welcome home, John. Welcome home."
After the battle, Sheridan is wanted in EarthDome. Franklin is heading to Babylon 5, hoping to stop Marcus, and Delenn has some business to attend to.
In an ISN special report, the reporter last seen on the air when ISN was taken over by forces loyal to Pres. Clark ("Severed Dreams") is overcome with emotion as she welcomes back their viewers and reports on the events of the past hours, alluding as well to her imprisonment and those of other colleagues.
Meanwhile Franklin continues to try to contact Babylon 5. He reviews the logs that Marcus downloaded, in which Franklin mentions the alien healing device and indicates that to save someone from fatal illness, the other person connected to the machine must die.
Aboard Babylon 5, in MedLab, a guard lies unconscious on the floor. Marcus has connected himself and Ivanova to the healing device. As he loses consciousness next to her, Marcus whispers: "I love you."