ISN is back on the air, as a mouthpiece for the Clark Administration. Franklin (Richard Biggs), Garibaldi (Jerry Doyle), and Ivanova (Claudia Christian) watch in disgust. Sheridan (Bruce Boxleitner) tries out the new Starfuries and receives a signal from an Earth Alliance vessel near Babylon Five. He investigates and finds it is a Black Omega Starfury, with Bester (Walter Koenig) inside. Bester says he is approaching this way so as not to be fired upon by Babylon Five. He asks to talk to Sheridan, who tows him in.

G’Kar (Andreas Katsulas) confronts Ivanova about her promise to have him appointed to the anti-Shadow alliance called the War Council. He’s tired of waiting. Bester boards the station and finds an armed Security team waiting for him. Sheridan sends Ivanova to him first, since she will know if he scans her. Bester tells her he thinks President Clark is under the control of Shadows, whatever they are. They have also infiltrated Psi-Corps and he wants to fight them. He’s certain the council at Babylon Five knows what they are.

Delenn and Sheridan talk of G’Kar and his loyal people. Delenn is heart-broken that she was silent when the Shadows helped the Centauri conquer his world. Sheridan and Ivanova take Bester aboard the White Star to find the Shadow vessel Bester believes is nearby. He can sense it. Delenn confesses to G’Kar that the Grey Council knew of the Shadow-Centauri alliance and said nothing. If the Shadows had found out what the Minbari knew about them, they would have attacked and the Narn would likely have been wiped out rather than conquered. The White Star engages the Shadow ships, destroying the support fighters and seizing the weapons transport. The Shadow warship unexpectedly departs. In the transport are Psi-Corps cryotubes.

On Babylon Five, Doctor Franklin examines the hundred telepaths in cryonic suspension, Sheridan confronts Bester, who admits he knew something, but not much. A woman in a capsule wakes up and screams to get out. She is released and then put to sleep. Sheridan shows her ID bracelet to Bester. As he is explaining, he sees her name, Carolyn Sanderson (Joan McMurtrey) and demands to see her. However, she has taken over Medlab and interfaced with the computer.

She recognizes Bester but attacks him. Garibaldi realizes she is reacting to his Psi-Corps badge and takes it away. She calls Bester by his first name and asks him what they have done to her. She shows him images of aliens experimenting on her. Later, Bester reveals to Sheridan and Ivanova that Carolyn was his lover. He begs them to save her, promising to help them fight the Shadows. Delenn brings G’Kar into the new command room. Garibaldi learns from the Book of G’Quan why the shadows killed all the Narn telepaths ages ago—Telepaths are a threat to the Shadows. Ivanova realizes that Bester sent the Shadow ship away by himself. And she reports that the Shadows are openly on the attack in Brakiri space.

The aliens experimenting on Carolyn were the Zener, the chief scientists of the Shadows. They are related to the Greys that kidnapped Terrans in earlier centuries. The Vorlons created human telepaths in the 22nd Century. The Ship of Tears, involved in the forced relocation of telepaths, comes from the Trail of Tears, involved in the forced location of American indigenous peoples. Bester’s delight in sitting in the Captain’s chair is a nod to his other well-known character, Pavel Chekhov.