"Second Sight" consists of two main story lines that converge at the end of the episode. The first involves Commander Sisko's falling in love with Fenna, a visitor to Deep Space Nine. The second involves the effort to re-ignite a star by Professor Seyetik and the Nebula-class starship USS Prometheus (NCC-71201, not the same USS Prometheus seen in the Star Trek: Voyager episode "Message in a Bottle").

Seyetik, "one of the Federation's greatest minds", has the responsibility of re-igniting a dying star to make it suitable for supporting life on an orbiting planet. He has arrived at Deep Space Nine to prepare for his mission. Meanwhile, O'Brien and Dax assist him. O'Brien is preparing the Prometheus, the starship Seyetik will use, for travel at Warp 9.6—in case of emergency during the mission, the Prometheus would need to escape quickly from the vicinity of the star.

In the other story line, Sisko meets Fenna while he's standing on the floor above the Promenade staring at stars out of a window. Fenna approaches him from behind and starts a conversation. After several moments, Sisko finds she has left him without a word. The two meet again in subsequent scenes during which they fall in love. Dax is apparently aware of their relationship; she comments to Sisko about it. It is the first spark of love he has felt since the death of his wife Jennifer four years earlier.

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