"Captain's Log, Supplemental: We're en route to the Grey Research Facility after receiving an urgent distress call. All attempts at long-range communication have failed."

While enroute to diplomatic negotiations on DS9, Admiral Nechayev and her away team of Excelsior personnel are kidnapped by pirates commanded by rogue Starfleet officer, onboard a stolen Federation starship. Meanwhile, Captain Shelby takes the Excelsior to assist the Cardassians in identifying where the pirates work from, as tensions with the Son'a increase.

"Captain's Log, Stardate 57324.6: With the Yridian drug runners in custody, we've tracked their last visit to the Federation colony on Bovina VIII. It appears the Yridians weren't just smugglers, but users of the Orion's cargo."

Lieutenant Corey Aster and Ensign Andrew Barrett are temporarily reassigned to the USS Aldrin on a routine terraforming mission on the edges of the Briar Patch. But when they discover a mass grave of hundreds of Bajoran refugees, they must look for answers when the Cardassians are implicated in their deaths. Aster grows close to one of the Cardassian scientists, and comes into conflict with Ro Nevin, especially since his grandfather was one of the victims of the massacre.

The Federation discovers suspicious fleet movements by the Tholians and believe it is a precursor to launching an attack to steal the Cardassian Tetrahedron. Attempting to warn the Cardassians and make preparations to join forces to stop it falls on deaf ears. The Federation decides to lay in wait outside of Cardassian space for the attack they are certain is coming.

The Independence prepares to become the first starship to enter and explore the subspace currents that allow warp travel in the Briar Patch. Officers from the Excelsior investigating strange readings on Ba'ku run into an old enemy. Dr. Henglaar faces some personal demons when his ex-fiancée, Independence Chief Engineer Sou, arrives on board with her husband, CMO Qu'Qul. But when Qu'Qul realizes his wife still has feelings for the Tellarite doctor, he challenges Henglaar to a Klingon ritual for Sou’s affection.