When Captain Janeway becomes aware of the situation, she decides to take the three young crewmembers on an away mission with her aboard the Delta Flyer. The first of the trio is Celes, an Astrometrics assistant who constantly has to have all of her work double-checked. Crewman Mortimer Harren has five advanced degrees in Theoretical Cosmology, but would rather spend his time down on Deck 15 and figure out the origin of the universe. Finally there is William Telfer, a Security Officer and hypochondriac who visits Sickbay weekly and is afraid of medication.

First and foremost, Janeway briefs the trio on their duties. Celes will be running an on-going sensor analysis and Harren will be looking for subspace particle decay which may offer new information about star formation. Meanwhile, Telfer will be on the lookout for any signs of life. Before they leave, Seven of Nine warns Janeway that an experienced crew would better serve the mission.

Not long into the mission, an invisible force suddenly strikes the Delta Flyer. Its propulsion has been knocked off-line and 90 percent of its antimatter has been neutralized. Harren suggests to Janeway that a comet-like assemblage of dark matter is responsible for the neutralization. Furthermore, he proposes that they eject their remaining antimatter in order to avoid another impact. However, according to Janeway, his theory is still an unproven hypothesis and she needs more convincing evidence.

Returning once again, Janeway decides to fire a photon torpedo at the force. Suddenly, the three crewmembers hear a humming sound and look on as Telfer begins to unexpectedly dematerialize and then disappear. Suddenly, he reappears and collapses to the floor and it appears as if something is writhing beneath his skin.

Janeway has no choice except to fire a phaser at Telfer when he reveals that the phenomenon is activating his motor neurons. As he struggles to stay on his feet, a stick-like, segmented entity extends out of an incision wound on his neck. The entity flings itself onto a console and attaches itself to the surface. Harren immediately aims the phaser, but Janeway instructs him to hold his fire. Ignoring the Captain's order, Harren fires and vaporizes the entity. Frustrated with Harren, Janeway suggests that the entity was simply trying to communicate with the crew.

Janeway decides to lead the Delta Flyer to a nearby planet where she hopes to reinitialize its warp core. Suddenly, a slow-moving swath begins to open up in the glowing particles of the planet's radiogenic ring. An unknown force is heading toward the vessel.

Janeway instructs her crew to get into the escape pods and to plot a course away from the planet. However, Celes tells Janeway that a crew never abandons its captain. Suddenly, Harren releases one of the escape pods and heads toward the swath while inside. Over the com, he tells Janeway that it will allow the Delta Flyer some extra time to make an escape. Janeway decides to go after the pod instead. Just a split second before it collides with the swath, the Delta Flyer's transporters lock onto the pod. The Delta Flyer then begins to fire phaser volleys at the glowing ring behind it, igniting a chain reaction of blazing, exploding light.

Suddenly, the Flyer begins to shake as bright light pours in the windows. The vessel is rocked hard and a blinding white light flashes outside the windows.

Next, a confused Janeway wakes up in Sickbay. Chakotay reports that Voyager received her initial distress call and found the Flyer drifting above a gas giant with everyone unconscious inside. Janeway tells Chakotay that the Good Shepherd went looking for a few lost members of her flock and ended up running into a wolf. However, in the end, the Good Shepherd did find them.