Londo Mollari (Peter Jurasik) is returning to Babylon Five, complaining of the growing chaos following the rebellion against President Clark, not to mention the fact that the Narns are now in charge of security. Overhearing this, the Narn checking ID cards decrees that Londo’s is not working properly and needs to be confirmed, which may take a few hours. Meanwhile, the EAS Alexander, now commanded by Major Ryan (Bruce McGill) is trying to hold off an attack by the EAS Clarkstown. Reluctantly, Major Ryan destroys the Clarkstown. Needing repairs, he must go to Babylon Five.
Sheridan (Bruce Boxleitner) calls a meeting of the command staff, informing them that the Alexander is coming. They decide that, when the ship arrives, they will shut down all but their official info channels. Lennier (Bill Mumy) brings Doctor Franklin (Richard Biggs) to a docking bay, where Delenn (Mira Furlan) is caring for a wounded Minbari Ranger hiding from bounty hunters. G’Kar (Andreas Katsulas) appears and offers to take him by a covert route to Medlab. Sheridan watches ISN and learns the provisional government of Mars has defied martial law. The Alexander comes through the jump gate and Sheridan shuts down the Babylon Five channels, except ISN.
In Medlab, the Ranger relays a message to Delenn: Some of the League of Non-Aligned Worlds are joining the Shadows out of fear of the Centauri and are becoming conquerors themselves. Delenn learns that the Minbari Grey Council intends to do nothing about this. Major Ryan arrives on the station and reports to Sheridan that General Hague is dead and Ryan has assumed command. Some Earth Senators have gone into hiding. Martial Law has reduced street-crime and some welcome it. Any dissent is crushed and ISN is laying low. Earth Starfuries are bombing Mars. Delenn leaves for Minbari to confront the Grey Council.
A jump point opens and the EAS Churchill appears, commanded by Captain Sandra Hiroshi (Kim Myori), who has urgent news for Ryan and Sheridan. ISN reports that Orion VII and Proxima III have seceded from the Earth Alliance, and then goes off the air. Captain Hiroshi reports that Clark is sending elite forces to seize other Alliance colonies. The Agrippa and the Roanoke are on the way to seize Babylon Five. Ryan and Hiroshi return to their ships and the command staff meet, deciding to fight rather than surrender.
Sheridan gives orders to prepare, including telling Ivanova (Claudia Christian) to contact Draal on the planet below so he can prepare the great machine if they need it. Delenn forces her way into the Grey Council. If the covenant made with Valen to fight the Shadows is broken, the Grey Council is no more. When she leaves, she is accompanied by five council members from the religious and worker castes. Sheridan manages to get through to his father. The whole of Babylon Five is armed and ready. He announces to the station that Babylon Five is seceding from the Earth Alliance. Only one person in command opts to leave. Sheridan sends Ivanova out in a Starfury to take charge of the fleet. The jump gate opens, and the Captain of the Agrippa orders surrender. The Alexander and the Churchill launch fighters in response.
Sheridan locks down the station, closes the blast doors, and arms the defense grid. A space battle follows, and Brown 95 is breached. The Narns attack the invaders. The Churchill, damaged, rams the Roanoke, destroying both ships. Ivanova’s Starfury is hit by another fighter and she ejects. Babylon Five and the Alexander destroy the Agrippa. The jump-gate opens and three Minbari Sharlin-class War-cruisers, plus the White Star, commanded by Delenn, emerge. She warns the Earth-ships that the only Earth Captain ever to win an engagement with the Minbari, Captain Sheridan, is under her protection. The Earth ships jump away.
After the battle, Ryan departs to seek out other Alliance ships to join up. Sheridan agrees to take on the Starfuries of the lost Churchill, and he abandons his Earthforce uniform. Garibaldi (Jerry Doyle) observes Earthforce personnel, including Nightwatch, leaving the station. Delenn arrives and Sheridan kisses her hand. Everyone in the Zocalo gives the commanders a standing ovation.
This episode—at the midpoint of the five-year run—won the 1997 Hugo Award, beating out Star Trek: First Contact, Independence Day, and Mars Attacks. Robert Foxworth was unable to return as General Hague because he was working on Deep Space Nine, so he was replaced with Bruce McGill as Major Ryan, who said in an out-take, “General Hague is Doing Deep Space Nine. He was double-booked by his agent, so you’re stuck with me.” Actually, it was Everett McGill that Straczynski wanted, but forgot his first name and asked for that McGill guy, so he got Bruce McGill instead, who worked out fine. Jerry Doyle had just been filmed breaking his leg when he broke his arm on set. He called the episode Severed Limbs. Sheridan and Delenn both got to make great speeches. Even the ISN reporters did the right thing before being shut down.