In season four, the station continues to serve as a refuge for heroes, thieves, and rare and exotic beings in a time of uneasy peace and the constant threat of war. The space station and its allies finally engage the powerful Shadows in a tremendous showdown, while the station's captain strives to expose far-reaching corruption on Earth. Also, Sheridan and Delenn's alliance – both personal and political – signals a new age of peace in the universe.
In the aftermath of the explosion on Z'ha'dum, Sheridan is presumed dead and Garibaldi is missing. Delenn struggles to keep the alliance against the Shadows together, and Londo takes up his new position on Centauri Prime as security advisor to the emperor.
On Z'ha'dum, Sheridan floats somewhere in-between life and death. Meanwhile G'Kar risks imprisonment to try to find Garibaldi.
Ivanova and Marcus take a White Star out to search for more first ones to aid in the war, while Londo tries to convince G'Kar to swallow his pride so Cartagia will find him entertaining. A mysterious spacecraft makes its way towards Babylon 5.
With the Vorlons destroying whole worlds, Babylon 5 is struggling to cope with the refugees. And with one Vorlon aboard, they cannot make a move without them knowing about it. So Sheridan decides to kill him. On Centauri Prime, Cartagia explains to Londo how he will become a god when the Vorlons destroy the planet.
As reports that the Shadows are destroying planets too start to come in, Sheridan prepares for one final showdown with the Shadows and the Vorlons. Meanwhile on Narn, Londo makes everything ready - G'Kar's chains have been weakened... an undetectable weapon has been acquired... Tonight Cartagia must die.
In the hours before the Shadows and the Vorlons meet Sheridan's alliance at Corriana 6, Ivanova and Lorien search for the last of the First Ones, and Londo races back to Centauri Prime in hope of removing all Shadow influence before the Vorlon planetkiller arrives.
Bester comes to Babylon 5 with information about President Clark's plans to discredit the station. But it has a price tag attached - he wants them to go to Z'ha'dum to look for any leftover technology that might help revive his lover. Garibaldi resigns his position as security chief.
A team of ISN reporters arrives at the station wanting to do a story about Babylon 5. Sheridan refuses at first, but finally agrees on the theory that at least a small part of their side of the conflict will be shown.
When her clan has doubts about her reason for taking Sheridan as a mate, Delenn is required to go to Minbar to attend "the Dreaming". Sheridan sends Marcus and Franklin to Mars to make contact with the resistance there.
Marcus and Franklin meet their liaison to the Mars resistance, but are greeted at gunpoint by the resistance itself. Meanwhile Sheridan confronts Garibaldi about his attitude.
Delenn investigates attacks on ships of races allied with the Minbari, and encounters the Drakh for the first time. On Mars, Franklin rallies the resistance leaders to Sheridan's cause.
Garibaldi gets his first assignment from his new employer - helping someone getting on and off the station without having to pass through customs. He is quite surprised at who this person is. Meanwhile Ivanova makes preparations for the first broadcast of "The Voice of the Resistance".
Sheridan hatches an eccentric plan to convince the League to accept White Star patrols on their borders, while Delenn seeks help from Neroon to end the civil war that has broken out on Minbar.
The warrior caste has surrounded the religious caste's stand in the capital city on Minbar, and demand they surrender or be destroyed. Meanwhile Bester makes Lyta an offer for her body.
With Clark having killed 10,000 unarmed refugees, Sheridan once again mobilizes for war. The first target is Proxima 3, which is being bombed into submission. At the same time, Londo tries to get G'Kar to partake in a joint Centauri/Narn statement in support of the war against Clark.
As Sheridan's forces continue towards Earth, Garibaldi is finally allowed to meet his employer, William Edgars, face to face on Mars, and is after telepath assisted interrogation finally told what he must do to gain Edgars' complete trust. Meanwhile Dr. Franklin discovers that Lyta can influence the Shadow modified telepaths.
After arranging for the arrest of Sheridan's father, Garibaldi gives his former commander the news, and urges him to come to Mars to arrange a rescue operation. But Garibaldi drugs Sheridan as soon as he gets there, and hands him over to Clark's forces. Finally, Edgars reveals his plans to Garibaldi.
In a bleak room, an interrogator tries to force Sheridan to admit he was under alien influence and worked to undermine Earth.
Garibaldi is barely able to convince Lyta and Franklin that his recent behavior was caused by Bester, and they organize a rescue for Sheridan. Meanwhile, Ivanova gets word that a trap has been set at the fleets' next rendezvous point, by a group of completely new advanced-technology destroyers.
The only obstacle remaining between Sheridan and Earth is a fleet near Mars. With the help of the resistance, Sheridan plans to smuggle Shadow modified telepaths onto the fleet, hopefully disabling it long enough for him to take Earth. Meanwhile, Marcus is determined to find a way to help Ivanova.
Clark is dead and the civil war is over, but several issues are unresolved. Ivanova is grief struck at Marcus's death and Lise is missing. And Sheridan must now face the consequences of his actions. He did the right thing - but in the inconvenient way.
Far into the future, someone is archiving video clips pertaining to the fate of Earth and the Interstellar Alliance.