To better understand the tetrahedrons operation, an interrogation of the Orion Syndicate pirate Mason is conducted. When he reveals the location of another tetrahedron key, a mission is set up to retrieve it, with his help. But one of the officers will not return, and the others will be left reeling at the loss of one of their own. Shelby encounters a few ghosts of her own, when assigned to assist a Romulan fleet make the necessary adjustments to traverse the Patch, and runs into her former lover, Captain Mackenzie Calhoun.

The stunning conclusion to the Star Trek: Hidden Frontier series. The Station is under siege by the Grey once more, as the crew of the USS Helena struggle to catch Siroc before he arrives at the Dyson Sphere. While the battle rages outside, Shelby and Lefler are leading a skeleton crew of 93 in a desperate ploy to restore the USS Excelsior and rejoin the fight to protect the station's civilians. With time completely gone, all hope lies in Admiral Knapp, Martinez, Jorian (Zen) Dao, Corey Aster and Jenna McFarland being able to figure out how to use the Hybrid ship; but things are far more different - and deadly - than they seem. With Ro as their captive and unwilling source of the technical data needed, Siroc and Betras arrive on the Dyson Sphere, and Siroc will stop at nothing to get to the secrets of the Dyson Sphere. Tolian Naros, along with Faisal, Henglaar, Elbrey, and others also arrive to try to rescue Ro Nevin and stop Siroc from bringing on the potential destruction of the universe.

Shelby's recovered the hearts and minds of Starfleet's allies against Siroc and the Tholians - but it may be too late. With the return of an old friend and the loss of new ones under tragic circumstances, Excelsior is in a desperate race to get back to her home station, as the entire patch has suddenly gone deathly silent. If things weren't bad enough, it has come down to the wire for Naros' race to beat Siroc to the Dyson Sphere and stop him from carrying out his mission. With Ro's capture, Siroc's entire checklist for his final plan is complete, and using the stolen memories from Counselor Elbrey, all that's left is getting there first.

Captain Shelby's leadership of the Allied forces is questioned, and Shelby is ordered to rest. Corey and Nevin consider an affair. Admiral Knapp, Pelas, and Lieutenant McFarland continue the search for Traya with no luck. S'Tal and Lieutenant McCabe miss Andrew. Captain Naros and Jorian Zen continue the search for Tesla Mor.

When sudden and brutal attacks by the Tholians and Breen begin to target both Starfleet and civilian craft alike, Captain Shelby must begin to battle for the hearts and minds of the Federation's closest allies. Meanwhile, Admiral Cole is confronted with overwhelming odds and an increasingly restless civilian crew in a desperate battle to survive.

The Allied fleet makes further preparations to counter Siroc's next move, whatever it may be. But with the Grey continuing to be a no-show in the struggle for the tetrahedrons and Dyson Sphere, the fate of Admiral Knapp's daughter hanging in the balance, and Barrett's friends still struggling with his MIA status, things are beginning to rush headlong into a breakdown.

The battle has been lost, and now the crew of the USS Excelsior struggles for their lives. With the battle plan shattered, and the enemy manuvering to annihilate them, no one is safe from the clutches of Siroc and the Tholian Assembly.

Knapp and Naros lead the Antietam on a surveillance mission that gets out of control, while Zen and Aster's relationship is threatened by someone from the Trill's past.

"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."

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.

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.

In preparation for the major attack the Alliance is about to undertake, Knapp promotes Naros to the command of the USS Helena, while taking command of the fleet itself from Excelsior. Realising Siroc may try anything to get to the Grey Dyson Sphere, Naros realises not is he a target, but so are Elbrey and Artim, while Shelby works on making sure her senior staff deal with the raw emotion of the loss of one of their own. Meanwhile, Siroc sets his own plan in motion to disrupt the incoming attack forces.

Learn what life is like aboard Deep Space 12, as Excelsior's crew copes with the stress of battle ever looming on the horizon. This episode is primarily focused on character interaction; however, it can be said to contain three separate "threads" running in parallel.

"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."

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.

During the final push of the Dominion War, Captain Ian Quincy Knapp, commanding the USS Devonshire, encounters an unknown, powerful, and malevolent new force in the McAllister Nebula.

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

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.

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 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.

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.

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.

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.

"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."

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 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.

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.

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.

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.