A joint exploratory venture from the Alpha Quadrant awakens in the Delta Quadrant, crew injured, ships damaged and the Klingons of their expedition gone entirely. Assistant Chief Engineer Zesh sh’Qiaqirn is one of the first to awaken, finding her superior officer sealing off a coolant leak as his final act. Now acting Chief, Zesh has the unenviable task of getting the ship back in working order while the ship figures out what happened. The captain does some inventory – the chief of security is injured, several others are hurt, and the ship is barely functional. Their Klingon allied ship is nowhere to be seen, but they find the Tiro.

The Romulan scout ship comes aboard, and they are met by a Talaxian scavenger named Skrillix. He offers to take them to the nearby world Sikaris 3, where the locals are famed for their hospitality. They are greeted there by Magistrate Gathorel Labin, a genial man who offers to assist them with determining a course home, and offers up a liaision in Eudana, a scientist.

It is Eudana who assists the crew of the Odyssey in determining what brought them here – Sikarian technology, used without approval. They confront Gath, who explains that he did so out of desperation, for his people are soon to be overrun by the Kazon. A scout ship arriving in the system puts truth to his admission, and the captain recalls the crew. Red alert.

The scout retreats, giving the gathered defenders a few scant hours to strategize. Several smaller ships and a larger Predator-class carrier are coming. The Odyssey opts to move out to meet them, leaving the Romulan scout ship cloaked in orbit with a mixed Romulan/Starfleet crew to cover the Sikarians’ planet directly. The Sikarians work to evacuate their people via the trajector technology that brought the Odyssey and others here. The Starfleet crew is tired and still wounded, but they’re ready to help. Skrillix is even issued a burgundy uniform and is assigned to the helm for the fight.

The fight is joined in earnest, and it’s soon realized that the Odyssey, while no slouch in a fight, can’t go toe-to-toe with the Predator. Sickbay is hit with a lucky shot, costing the ship its Chief Medical Officer and medical staff. And as the Odyssey holds on and uses some of its superior technology to hold the Kazon at bay, they opt to use boarding shuttles to get aboard the Starfleet ship. In the melee, the first officer is grieviously wounded.

As they hold off their attackers, the Odyssey detects Gath and his loyalist cronies sabotaging the trajector – their way home. Captain Tchang beams Gath aboard and determines that Gath’s deal, sending them home after the Sikarian people flee, was never due to be honored. Eudana, realizing this as well, gathers the last 15,000 of the Sikarian refugees into the last civilian ships and leaves for orbit. Rather than handing the trajector technology to the Kazon, the Odyssey fires two tricobalt torpedoes at the trajector facility and turns to start the long trek home. The Sikarians join them.

The Odyssey parts from the convoy briefly to collect fuel at a nebula carrying deuterium and showing signs of omicron radiation. When they arrive, they find an unusual energy barrier within the nebula, and a ragged opening. Within, a cargo freighter had attempted to cut through the nebula with similar intent to the Odyssey. It crashed through the barrier, encountered some sort of nonconductive biogenic material, and got bogged by it more than 60k kilometers inside. Too deep for transporters, too delicate for a tractor beam, and the freighter captain insisting upon his ship remaining intact, the crew opts to send a shuttle in before the energy bursts happening randomly in the nebula strike the freighter and destroy it.

Lieutenant Commander T’Ven, the ship’s tactical officer, requests to lead the mission. He has just awoken from a healing trance after injuries sustained in the initial trip to the Delta Quadrant, and is eager to be of use. Lieutenant (JG) sh’Qiaqirn and Lieutenant (JG) Hobbs from Engineering travel with him. At the last moment, Subcommander Selveth of the Romulans, feeling at loose ends, insists upon going as well.

With some clever engineering work, and piloting assistance from Commander T’Ven, the shuttle is used to jumpstart the freighter, and then the freighter pulls itself free of the barrier. Selveth explains that the barrier is the cocoon, or eggshell, of an enormous spaceborne lifeform. Their intrusion into its incubator will not harm it. As thanks, the freighter captain personally provides Lt. sh’Qiaqirn with a pair of his specially-made power conduits for her to reverse-engineer.

As the Sikarian convoy waits in an uninhabited system, the Klingon ship Jor, separated from the Odyssey in the initial transport to the Delta Quadran, appears. After a blitz attack damages the convoy’s largest ship, they send out a distress signal to recall the Odyssey while they hide in the atmosphere of one of the planets. A tense stand-off occurs when the Starfleet ship arrives, eventually broken when Captain Tchang and Commander Klaa of the Jor agree to continue honoring their alliance from the Alpha Quadrant. Klaa is unimpressed by shepherding the Sikarians, and sends his second, ship’s surgeon Plogh, to observe the situation with repairs on the planet below.

While Tchang and Plogh discuss the situation and the fact that Gathorel Labin is aboard the ship getting repaired, the Kazon arrive and attack from orbit, launching a few landing pods to attack the repair teams. Tchang, T’Ven, and Plogh, along with a few security staff from both ships, take down the Kazon attack with ease and return to their ships, recognizing another running fight in their near future.

Taking what he’s learned so far from their fights with the Kazon, T’ven opts to focus fire upon the Kazon’s sensor arrays, making it impossible for their more powerful weapons to make a clean hit. The Jor joins in this, crippling the bigger Kazon ship handily as a swarm of smaller ships head for the Sikarians. The Odyssey begins swatting their engines, and the Jor is struck by a lucky shot from the carrier, crippling her. Klaa calls for the Jor to ram the Kazon carrier, seeking an honorable death in combat. Seeing an opportunity for the young Klingon crew to earn more honor than in death, Plogh covertly signals to the Odyssey their situation, and joins his crew in being beamed off the Jor seconds before it crashes into the carrier and explodes.

A few weeks’ travel has the ship arrive at Zill’gan station, a neutral trading station and repair yard. The administrator, Jojjal, authorizes a berth for all the ships on the convoy while they barter. Ultimately, a large quantity of replicated water buys their way aboard and use of the repair facilities.

The crew spreads out in order to find parts for their sickbay, and hydroponic plants. They locate an Ocampa merchant who sells them (of all things) Earth potatoes and onions. And then weird stuff starts happening, starting with the trading crew losing several hours. Chroniton bubbles are appearing randomly aboard the station – shifting time within the bubble forward or backward.

Via tricorder and triangulation, the crew finds that a piece of tech hidden on a portion of the station given to pirates is the reason for this. They get involved unofficially via Plogh and Skrillix showing up as independent troubleshooters, warning them. They ask for help – and Zesh swings in to disarm the machine.

The Tiro heads off on a mission to Banea, where the locals have some renown as astrophysicists and builders of space telescopes of exceeding accuracy. As the planet is being blockaded by its neighbor, the Tiro goes, with Tchang, T’Ven, and Plogh along with the Romulan pilot, Pabian, and a noted astronavigator from each faction in the convoy.

Upon arrival and insertion past the convoy, the crew meets Tolen Ren, leader of the scientific institute collecting information on nearby space. He had been seeking information on the blockade from anyone with the ability to collect it, as their telescopes had been ordered shuttered to prevent hostility with the blockading Numiri. The captain offered the Tiro’s scans in exchange for star charts, and Ren was only too happy to oblige. While they gathered the data, Ren hosted a meal for the scientists and the crew to converse, and learn of each other.

That was interrupted by an attack by terrorists, who stunned most of the scientists and crew, including the captain. However, T’ven protected the crew, flipping tables and stationing himself near the captain. And Plogh managed to take a hostage, who explained the situation. The Numiri and Baneans have been fighting border wars for years, and the Numiri wanted plans for an interstellar torpedo targeting system, something Ren inadvertently created and buried.

The captain woke up, and got involved. Convincing all involved to task their government, the Numiri allowed the Odyssey to approach in order to facilitate negotiations. It took most of a month, but at the end of things, the Odyssey flew away from Banea with its goal, and with the potential start of peace between these two species.

Approaching a cluster of stars unique for their density of Class-M worlds, the convoy opts to take some time to explore the cluster’s worlds. The Posel and Odyssey stay on course, though they slow for the scattered ships to return. While they travel, the Odyssey opens the holodecks to the Sikarians, allowing for as much leisure as possible given the circumstances.

This is all cut short when the ship receives a garbled, barely-legible distress call – a woman indicating that their ship’s warp drive was damaged and they were stranded in space. The Odyssey jumps to the rescue, leaving the Posel to continue on-course.

As they approach, the visual sensors give the crew pause – the distress call is coming from a Predator-class carrier, the big planet-killer ships the Kazon have wielded against them to dire effect twice before. This one was stricken though, with obvious damage and leaking theta radiation. As they wonder at the possibility of a trap, Sebastian brings the Kazon prisoners taken on the Class K planet up to the captain – one has been asking after her.

She meets with the boy, named Kemman, and gains perspective on the Kazon. She asks for Kemman’s help in rescuing his people, and while they are from a different sect than the boy, he agrees. T’ven, Plogh, Lt. Hobbs, and one of the Klingon bekks beam over with Kemman and locate the one who sent the distress signal. It’s another Kazon child, this time a girl named Heklara. Plogh inoculates her and the friends she reveals against further radiation, and realizes that the children have survived due to an evolutionary process that the adults of their kind lose. Hobbs gets transporter pattern enhancers set up and assists T’ven with downloading the contents of the Predator’s database.

The away team is able to beam most of the children to safety via the enhancers, but secondary explosions from the damage to the Predator begin taking apart the ship, destroying too many of the enhancers. Left with only one option, T’ven leads the team and the remaining children to the Raider docked with the Predator. After a harrowing journey, they get aboard the Raider, dislodge from the docking clamps, and blast away as the Predator finally succumbs to its damage.

Back on the Odyssey, they detect Kazon coming to investigate the distress signal. The captain asks Kemman and the crew for options, and settles upon getting the children home to their people via the nearby Class M planet. To assure they are taken home, she leaves a Type-9 shuttle and two volunteers behind, with orders to catch up when the Kazon retrieve their children.

The convoy parks near a binary pulsar to allow the Odyssey to try an audacious plan – using a pulsar in sight of the Federation’s telescopes to send a one-way message. Lieutenant Annira, the mastermind behind the idea invites Lt. Cat Domino, the ship’s flight controller, to aid in both the construction, and calculation of the trajectory to send the message.

Meanwhile, the Sikarians put on a tribunal in an attempt to further establish justice with regard to Gathorel Labin. Counselor Perrik interviews him, and the Captain is selected as an advocate for the victims. Commander Sebastian steps in as an advocate for the accused.

While the tribunal progresses, T’Ven oversees the disassembly of a shuttle to fortify the captured Kazon Raider. It’s decided that the Klingons will crew it, rotating between it and the Odyssey. While working, a bekk named M’rek joins the work, despite lacking technical skill.

A strange collection of exotic particles leaves the message project on hold while Domino and the Romulan astrophysicist Vulmos investigate. In typical Romulan style, Vulmos assumes a threat, whereas Domino hypothesizes it may be chaotic space interacting with ours.

She turns out to be right, and her experience with the phenomenon reveals that this is an indication of a weakening in subspace originating farther away, and that this is just a unique circumstance, a trimetric fracture. With no immediate threat, the pair work to circumvent its effect on their message home.

The tribunal involves intense interviews with Sikarians, Ensign Barnett, and an impassioned plea from Commander Sebastian. Finally, after discussion as a group, the chosen Advocates opt to believe in a person changing, and prepare to find him a role somewhere in the convoy.

However, the suspicious bekk prompted T’Ven to involve Plogh, and the pair narrowly miss the assassination of Gathorel. While initially, evidence points to M’rek, dogged investigation reveals a desperate Romulan named Kumir framed M’rek. The tribunal is rendered moot, and the Sikarians struggle with the end of the situation.

Finally, Domino sends the message, utilizing the trimetric fracture to amplify the signal. The Starfleet members (and Selveth) send messages home. The Klingons pool their character limits to send back a poem glorifying their dead commander.

With their one-way message sent, the convoy warps away.

After tracking a Kazon fleet pursuing them, the convoy speeds up – and the Kazon do too, slowly catching up. After three days of steadily closing the gap, the crew meets to discuss options. Engineers across the fleet need time to manage their engines – a half day, likely.

Domino suggests an audacious port of rest – a rapidly dissipating plasma storm. They take refuge within. Simultaneously, they launch a modified probe broadcasting the Odyssey’s warp signature. This only fools the Kazon momentarily, giving the crew pause. That concern deepens when a Kazon scout is detected waiting for them outside the storm.

An investigation reveals that someone aboard is passing information to the Kazon. Tensions rise when evidence points to the Romulans, but T’Ven and Domino spring a trap that catches a Sikarian posing as a Starfleet technician.

The spy contained for now, the Klingons pilot their stolen Kazon ship out of the storm, learning that the Kazon sects have united in order to capture and pillage the Odyssey. Having learned of the goal, and of their mole, the Odyssey and Klingon ship disable the scout, launch another probe, and use their mole’s secret channel to misdirect the Kazon behind them.

With a small amount of breathing room, the fleet races for the dark matter nebula that creates part of the border of Kazon territory. Kemman reveals that the nebula is occupied by restless spirits, and the Kazon avoid it. The Captain orders the Tiro ahead to scout the edge of the nebula and it finds a line of Kazon warships waiting for them.

Knowing they need to take their chances with the nebula, Captain Tchang arranges the fleet and runs the gauntlet. A well-times deflector pulse from the cloaked Tiro ignites an energy discharge in the nebula. The discharge gives them an opening, but also disables the Tiro. The fleet slips through the gap and disappears.

Captain Tchang wakes up to her daughter shaking her. She’s back on Starbase 364, the day the Odyssey left. Trying to shake the bad dream, she falls into the family moment. Elsewhere, T’Ven wakes, having a similar realization. In order to confirm his suspicions, he does a security sweep and finds Barnett, who he didn’t know about at launch. They bring their findings to Admiral Hebert, who postpones the Odyssey’s launch.

Plogh awakes on the Jor, which should be destroyed. He tries to scan for temporal anomalies without luck, before reaching out quietly to T’Ven. The pair begin investigating the situation fervently, especially as crew start disappearing without explanation.

After the Captain’s symbiont shows signs of having its neural energy drained, Plogh confirms – they’re all slowly being drained of neural energy. T’Ven, using mind melds that he is only somewhat trained with, is able to free the Captain, Plogh, and himself from the mass delusion. In the real world, the Sikarian spy had been possessed by an energy being and was leading them into the dark matter nebula to feed its brethren. Working together, the crew killed the possessed Sikarian, remodulated the shields, and raced through the nebula.

Once on the other side, the toll was counted. Many Sikarian casualties, several Starfleet ones, including a brain dead Annira. T’Ven, hypothesizing wildly, garners assistance from Plogh and one of the captain’s former hosts in order to mind meld with Annira and bring her back from the brink, sharing his neural energy with hers. Annira is in need of serious bed rest, but is expected to make a full recovery.

The fleet, ragged and tired, pulls into orbit of the planet Mondrea to seek respite to repair before moving on.