On board the EAS Agamemnon, Captain John Sheridan (Bruce Boxleitner) is finishing a mission when he receives a communication from General Hague (Robert Foxworth) telling him that the rogue Minbari warship, the Tragati, has been seen the past few days near Babylon Five. Though the Minbari are searching for it, the General wants Sheridan at Babylon Five just in case. But the President wants something more.

On Babylon Five, Lt. Commander Ivanova (Claudia Christian) records in the log that commander Sinclair was recalled to Earth five days previously. Chief Michael Garibaldi is still in critical condition in Medlab, and Minbari ambassador Delenn is in a chrysalis. The General informs Ivanova that Sinclair has been permanently assigned as the Earth Ambassador to Minbar, by their request, and that Sheridan will be the new commander of Babylon Five.

Minbari Grey Council member Hedronn (Robin Sachs) arrives at Delenn’s quarters and explains to her aide Lennier (Bill Mumy) that the Trigati is in the sector. Captain Sheridan arrives early and Ivanova greets him at Customs. She gives him a tour and explains some of the weird stuff going on, including the disappearance of Ambassador G’Kar (Andreas Katsulas). A Minbari warrior arrives in Green Sector. Ivanova shows Sheridan his quarters. He has worked with many of the species represented at the station, but the Minbari are still unhappy with him because of his role in the Earth-Minbari War. Hedronn recognizes the mysterious Minbari warrior as Kalain (Richard Grove), who has a particular disliking for Sheridan.

Sheridan begins his good luck speech to the C&C crew, interrupted by a Minbari message about station security. Kalain waltzes through Green Sector, knocking out a guard who tries to stop him. Hedronn meets with Sheridan and Ivanova and warns them about Kalain, who Sheridan assumes is in command of the Trigati. Kalain believes the Grey Council had betrayed Minbar, and Sheridan thinks he may be out for revenge on Delenn.

Kalain is in Delenn’s quarters, Lennier standing against him. Sheridan and a security team arrive and arrest Kalain. Lennier approaches Sheridan later to speak to him about the Battle of the Line—how Delenn ordered a star-pilot captured and interrogated. As he was being tortured, the Grey Council discovered that Sinclair had a Minbari soul. If Minbari souls are being reborn in Humans, the latter must not be destroyed, and the Grey Council ordered a full retreat at the hour of their victory. The Trigati comes through the jump gate, its weapons ports open.

A red alert is sounded, the Starfuries scrambled. The Minbari ship demands Kalain, but Kalain has committed suicide in his cell. Sheridan orders the Starfuries not to respond to the Trigati’s provocation. There is no battle. A Minbari ship searching for the Trigari comes through the gate and destroys the Trigari’s engines. The Trigari self-destructs.

Ivanova visits Sheridan and he confesses misgivings about his assignment. Lennier returns to his vigil and tells Delenn in her cocoon that he regrets not being able to tell Sheridan more—that a great enemy is returning and the Humans and Minbari must unite to defeat it. After he leaves, the chrysalis begins to crack.

This is the first episode of the second season, which is called The Coming of Shadows. Michael O’Hare (Sinclair) left because he was undergoing treatment for schizophrenia. Keeping his secret, J. Michael Straczynski replaced him with Boxleitner as Sheridan. However, Sinclair returned several times in cameo appearances in Season Three. Boxleitner is more dynamic than O’Hare, less cerebral and diplomatic. Bruce Boxleitner and Peter Jurasik (Londo Mollari) appeared together in 1982’s Tron. James Earl Jones, John Rhys-Davies, Barry Bostwick, Michael York, and Michael Moriarty were all considered for the Sheridan role. Captain John Sheridan was ranked Number Nine in TV Guide’s “25 Greatest Sci-Fi legends” in 2004.

Sheridan is descended from General Philip John Sheridan of the Union Army. Boxleitner is coincidentally a big Civil War buff. The Minbari call Sheridan Star Killer. He destroyed the Black Star with mines. They find it hard to let go of this. Caitlin Brown was replaced as G’Kar’s aide N’Toth by Mary Kay Adams and soon the character disappeared entirely. The cool blues and grays of Season One were replaced by reds and oranges for the more war-torn Season Two. The Agamemnon is named after the British warship commanded by Lord Nelson. If filming ran past 5:00 PM on Mondays during football season, the cast and crew began humming the theme from Monday Night Football whenever the director walked on set.