Season 2

Captain Knapp welcomes two representative of the planet Tren'La, who have had centuries of experiences with the Grey, Princess Illiana and her son, Aris. Fleeing a Grey attack, they appeal to the Federation for help, although Admiral Nechayev must turn down their request, despite the advantages their spatial fold drive may bring. But when Aris and recent Academy graduate Artim Ibanya discover Grey troops on Ba'ku, Knapp must take command of the fleet to fight off a Grey attack against Deep Space 12.

A glimpse at what could have happened if the original Excelsior, under Captain Hikaru Sulu, had found itself falling through a temporal anomaly on its way to assist Captain Kirk at Camp Khitomer. The Federation has fallen to the Borg, having been punished by the Q Continuum for their massive retaliatory strike against the weakened Klingon Empire after the assassination of the Federation President. What remains is being lead by the Battlestar-class USS Excelsior, as they search for a safe haven, but the arrival of the original Excelsior may provide a way to do more then simply survive.

Relationships with the Dominion come under threat when Captain Knapp is accused of killing a Founder serving as an ambassador to the Federation, while on a mission to help learn more about the Grey. Commander Shelby is put in the uncomfortable position of acting as the prosecutor in the informal investigative hearing held aboard Deep Space 12.

While transporting the Excelsior's new Security Chief, Lieutenant Luko, back to Deep Space 12, Lefler and her team are abducted by Orion Syndicate pirates who want her help in siphoning off a dangerous explosive byproduct of warp engines from a derelict Starfleet vessel.

Investigating the destruction of the terraforming vessel Encke in orbit of Osiris III, the Excelsior takes aboard Mission Specialist Corey Aster, an old Academy classmate of Ro and Rawlins. Ro is made uncomfortable when he realizes Aster still has feelings for him that he demonstrated while at the Academy, but the two are soon working together to identify what really happened to the Encke.

With the science mission on Ba'ku now under the control of Starfleet Medical, Ensign Artim Ibanya spends some time on Excelsior as he considers whenever to take a position on a science facility on Danula II. He tells Counselor Elbrey a tale of his life just before he went off to join the Academy, of how he became interested in Starfleet, met a young Lieutenant Jason Munoz, and foiled a plot of the Breen.

Luko rescues Traya, a young girl who happens to be Captain Knapp's daughter, from an Orion Syndicate slave planet, but come under attack from a squadron of Grey attack fighters. Excelsior manages to fend of an attack, but suffers damage that makes them unable to jump to warp. Soon, they are easy pickings for another Grey attack, which leaves the ship disabled and the crew, scattered throughout, attempting to avert a series of calamities long enough to restore power before a Grey battleship can move in for the kill.

An Andorian crew member is the only casualty when a conduit accidentally ruptures on the Excelsior. Radiation causes brain damage that results in a permanent case of clinical depression. While Henglaar looks into medical avenues to help the crewman and Counselor Elbrey does her best to keep him motivated, Captain Knapp also gets involved, lest the depression become too much and he becomes a danger to himself, and others around him.

Aris and Illiana are stunned when Kaz, Illiana's husband, arrives at the station, but he brings news of a massing Grey armada. As Starfleet prepares to intercept the threat, Captain Knapp is relieved of command of the Excelsior, while a Board of Inquiry prepares to judge his conduct regarding the damage Excelsior took while rescuing Traya during the events of HF 2.07 - "Fire In The Heart".