The mysteries of the Briar Patch beckon to the crew of the USS Excelsior, under the command of Captain Ian Quincy Knapp and his new senior staff. Their first mission has them looking for an foe that Knapp already has some knowledge of, but what they will discover will shock them all.

The Excelsior leads a task force after the Grey, but her crew quickly realizes they got more than what they bargained for!

The Independence is caught in 29th century intrigue when the crew discovers a legendary event in the past may have occurred due to tampering with the timeline.

Captain Knapp briefly clashes with new XO Elizabeth Shelby's attitude, before the Excelsior heads off to investigate the disappearance of the Nova-class USS Perihelion. Arriving at the ship's last known coordinates, they discover the ship in an impossibly close orbit of a quantum singularity, alongside an unknown vessel that dwarfs the Excelsior. But when an investigation reveals the strange, deleterious effects that the singularity had on the Perihelion crew and now the Excelsior crew as well, they realize what the ramifications could be for the entire galaxy.

The Grey are back, but the only one who can stop them may not be willing to help.

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".

With DS12 surrounded by three Grey battleships, Admiral Nechayev orders the shields fortified. She notes that they are not without resources, but Commander Darwin suggests that with the fleet away, they don't stand a chance. Knapp then reminds them that not all the ships are gone. Nechayev asks him if he has a plan - Knapp says he'd better by the time he gets to the docking ring.

The Grey battleships and Captain Knapp are trapped in fold space and the fleet has returned to Deep Space 12. While a debate erupts about whether they should attempt to recover the Captain without releasing the Grey, Commander Shelby and Aris mount a risky rescue operation that has long-term consequences.

The Independence becomes entangled in a cat-and-mouse game that leads them to ancient archaeological artifacts indigenous to the Briar Patch. Meanwhile, Commodore Knapp and Traya spend some quality time together on a shuttlecraft. Back on Deep Space 12, meanwhile, Lieutenant Commander Lefler is haunted by her capture by Sha'kev the previous year - the nightmare worsens when Sha'kev sends her a cryptic message of his imminent return.

After having a vision of a Borg attack, Corey Aster tells Counselor Elbrey of a mission he was on, while aboard the Olympus, when they encountered the Collective.

Son'a Ambassador O'Faur comes to DS12, engaging in an abrupt meeting with Commodore Knapp and Admiral Nechayev. She shows them an image of a Cardassian shipyard constructed within Son’a territory at the edge of the Briar Patch. When Knapp asks whether the Ambassador has lodged a complaint the Cardassian government, she notes that the territory is in dispute from before the Dominion War. She then threatens that if the Federation does not intervene, they cannot be held responsible for the consequences.

As Ian Knapp, Myra Elbrey and Traya Knapp are preparing to celebrate the Earth tradition of Christmas, a surprise visitor arrives on the station. Someone is keeping an eye on the Briar Patch and is not saying why.

The Excelsior is called in to mediate a dispute between two sets of colonists after the death of one of the Federation colonists in an accident. A fundemental cultural difference threatens everything they have built. Meanwhile Ro Nevin is struggling with the concept of a relationship with Corey Aster.

Encountering a Ferengi trader, Shelby authorizes Luko and Lefler to obtain an old Starfleet ship. Returning the ship to DS12, Lefler assembles a team to return the old ship to active status and are granted permission to take the ship out for a cruise. But things never work out simply when they receive a distress call, and find themselves the only available help for an endangered science vessel.

"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."

"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.