A probe launched by the Federation starship Voyager is stuck in the atmosphere of a gas giant planet; because of the value of the resources it has collected, the crew attempts to come up with solutions to recover the probe. Lt. Tom Paris presents the designs for a specialized shuttlecraft, the Delta Flyer, that he has been designing over the past few months that would be able to withstand the gas giant's atmosphere. The rest of the crew help to finalize the schematics. Chief Engineer B'Elanna Torres submits designs for the hull and propulsion systems, but seems uninterested in the project, and distant from Paris despite their ongoing romantic relationship. Even talking with Morale Officer Neelix and enjoying her favorite comfort food, banana pancakes, does not cheer her up.
The crew soon discovers that a Malon ship has discovered the lost probe, and they too are constructing a specialized craft to recover it for themselves. Efforts to build the Delta Flyer are boosted as it now becomes a race to recover the probe. As it nears completion, a structural flaw is discovered. Torres offers to test it via the holodeck, but purposely turns off the safety controls. The simulation shakes the virtual Delta Flyer and Torres is injured and knocked out from the test. While she is recovering, The Doctor diagnoses Torres with clinical depression. Captain Janeway discovers that Torres has been using the holodeck without safety protocols several times of late, and takes her off duty.
Torres' friend, First Officer Chakotay, attempts to learn more from her, taking her to the holodeck to revisit one of her programs that simulates the deaths of several of their Maquis friends. Torres explains that since she learned (via the recent personal information they got from the Alpha Quadrant) that many of their Maquis allies have been killed by the Cardassians and their new allies, the Dominion, she has been unable to cope with the trauma short of putting herself in near-suicidal danger. Chakotay promises that he and the crew will help her.
The Delta Flyer is finally completed, and Torres volunteers to join its crew, insisting that she be there to monitor the hull stability. The craft, along with the Malon one, race to the probe, but the Delta Flyer arrives first and retrieves the probe. However, on their way out of the atmosphere, the craft develops a hull rupture. Torres is able to create a makeshift forcefield to contain the rupture long enough for the craft to return safely to Voyager. She is commended for her actions, and celebrates with a plate of banana pancakes, finding herself experiencing emotion for the first time in several days.