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.

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.

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.

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.

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.