After the incident on Z'ha'dum, Sheridan is presumed dead, Garibaldi is missing and the fragile alliance against the Shadows is crumbling. Londo faces Emperor Cartagia. Babylon 5 is in a holding pattern, waiting for the next shoe to drop.
Sheridan has managed to get the Vorlons and Shadows into one sector, where they are not attacking each other directly. He and Delenn lead a fleet into the sector where the source of the conflict is finally revealed, this is the end of the Shadow War.
Delenn meets with Neroon to discuss the war that's torn their planet apart. She proposes a plan but she'll need his support. Sheridan launches an eccentric plan involving misdirection, rumors, etc, to get the League to agree to a new role for the White Star Fleet.
The Minbari war between the warrior and the religious castes comes to an end, leading to the formation of a new Grey Council. Bester comes to Babylon 5 to make Lyta an offer. Clark's forces attack a transport convoy carrying thousands of civilians, prompting Sheridan to change strategies.
After Clark's order causes the death of civilians, Sheridan decides it's time to attack Clark's forces directly. First mission is a colony that's being oppressed by some Earth Cruisers. Some in Earth force also distrust Clark, Sheridan might find some allies, amongst those he might be fighting.
Garibaldi meets with his benefactor. He wants to join with Edgar Industries. But his employer wants proof of his commitment. He wants Garibaldi to bring in Sheridan. Meanwhile Franklin finally manages to temporarily revive a telepath that had been captured by the Shadows. He'll need Lyta's help to continue his research.
Garibaldi, now freed of Bester's influence, tries to find allies to free Sheridan. But no one trusts him, not even those who used to call him friend. Now Garbaldi, Franklin, and Lyta try to free Sheridan. Meanwhile Ivanova and Marcus find out Clark has new more powerful ships. They take a contingent of White stars to destroy the new ships, someone will pay a high price for the victory.
The battle for Earth concludes as Sheridan leads his forces to Earth to confront Clark's forces in an all out battle. Meanwhile Marcus learns of the alien device Franklin used to heal Garibaldi when he was critically injured. But to save a person's life, someone else must die.
Earth is now free from Clark. Sheridan must now face the new President for his actions. He's forced to resign. Delenn, G'Kar, and Londo offer the Earth President a chance to join the newly formed Inter Stellar Alliance. Garibaldi searches for Lise. Ivanova revives and tries to deal with what her recovery cost someone else.