The film originally aired January 4, 1998 on the TNT cable network, a couple of weeks before season five of the series began.
Ten years before the television series Babylon 5 is set, Earth becomes involved in a deadly conflict with the just-discovered Minbari race. This war nearly leads to the extermination of the human race, but it is mysteriously halted at the last moment by the Minbari leadership for reasons that remain secret for over a decade. This near-destruction of the human race leads to the Earth Alliance creating the Babylon space stations as a means of preventing further wars.
Centauri Prime is in flames. A man surveys the destruction from a window of the Royal Palace. Two children, Luc and Lyssa, are later seen playing in the throne room and looking out the window. Their governess finds them and tells them that it is the Emperor's window and that only he can look out from it. The Emperor hears them and tells them to come in front of him. The Emperor is an aged Londo Mollari. Mollari allows Luc to be Emperor of the Centauri Republic for five minutes, during which time he may give any order he wishes. Luc asks for a story of great battles and heroes and villains. Lyssa wants to hear a true story. Mollari decides to give them both what they want and tell them the story of the Earth–Minbari War that happened 35 years ago while he was ambassador to Earth.
The human race, feeling cocky following their defeat of the Dilgar—is rapidly expanding into space. Word reaches them of the mysterious Minbari race. Though they are warned by Londo to leave this race alone, they seek to research the species first-hand.
The Minbari Grey Council, led by Dukhat, have become concerned that the Shadows may have returned to Z'ha'dum in fulfillment of Valen's prophecy. They are taking a roundabout route to investigate when they encounter Earth ships, specifically the Prometheus, seeking to investigate the Minbari.
The Minbari ships turn toward the Prometheus and engage their long-range sensors to gain more data on the unknown Earth ship. Unknown to the Minbari, the intense EMP field generated by their sensors disables the Prometheus' jump engine, preventing the Earth ship from retreating. As the Minbari ships draw closer, they open their gun ports—a sign of respect in their culture. The interference from the Minbari sensors also prevents the Prometheus from determining whether or not the Minbari ships are charging their weapons. The captain of the Prometheus, with his jump engines disabled and the Minbari ships approaching with apparent intent to fire, misinterprets this as a sign of aggression and opens fire. The Minbari ships are heavily damaged, and Dukhat is killed. In retaliation, the Grey Council declares a holy war against humanity, and the Earth–Minbari War begins.
The war lasts three years and countless humans are killed, their forces overwhelmed by superior Minbari technology. Lieutenant Commander John Sheridan, first officer of the EAS Lexington, is part of a battle group engaging the Minbari. After a Minbari ambush, Sheridan's commanding officer is killed. He assumes command of the damaged ship and lays a trap for the enemy, seeding the local asteroids with nuclear mines. The Minbari flagship Dral La Fi (Minbari for "Black Star") closes in to finish off the ship but is destroyed by the mines. This is Earth's only real victory during the war, and the faction of Minbari that feel the war has caused enough senseless bloodshed uses this as an opportunity to engage in peace talks with Earth. However, the Centauri intelligence division discovers that the Humans are having a secret meeting on a neutral planet that is being brokered by the Narn. Fearing the meeting will secure a shipment of advanced armaments to aid the Humans in their struggle, the Centauri bomb the peace conference, with neither the Humans nor Minbari suspecting their intervention. All hope for peace is lost, and humanity's destruction at the hands of the Minbari continues.
As a last, desperate effort to stave off the inevitable, the President of Earth orders all available ships to form a "line" around the planet in an attempt to delay the Minbari obliteration of the human race. This "Battle of the Line" is the final engagement of the war.
During the battle, Satai Delenn (Mira Furlan), a member of the Grey Council, abducts a human pilot, ostensibly to learn about Earth's defenses. This pilot is Jeffrey Sinclair (Michael O'Hare). The Grey Council is startled to discover, upon using the triluminary, that he appears to carry the soul of Minbari religious leader Valen. After examining several other humans, the Grey Council concludes that Minbari souls have been reincarnated in whole or in part in humans.
Since Minbari do not kill Minbari, they surrender to the defenseless Earth forces rather than kill Minbari souls in human bodies. Because of the damage this revelation could do to their own culture, they keep the reason for the surrender a secret.
In the wake of the war, Earth builds a space station that can serve as a kind of "United Nations in space", with the intent of preventing future wars. This is the Babylon Station, destroyed by terrorists during construction. Various fates befall later iterations of the station, until the completion of the Babylon 5 station and the pilot of the Babylon 5 series, set in the year 2257.
After the children leave him, Londo views Delenn and Sheridan being held captive in the Centauri palace "War Without End". Toasting them as his friends, Londo drinks massively to put his Keeper to sleep so that he can let them escape.
In the first season episode "And the Sky Full of Stars", a member of the Minbari Grey Council tells Delenn that Sinclair must be killed if he remembers his missing 24 hours at the Battle of the Line. J. Michael Straczynski has stated that this is not a contradiction, as unlike Kosh and Ulkesh (AKA Kosh II), the Grey Council did not know of Sinclair's destiny to travel back in time and become Valen, rather believing that it was the other way around. They had concluded that rather than see Minbari society destroyed, as they were not prepared for the truth about Valen at the time, it would be necessary to kill Sinclair if he remembered.