B'Elanna Torres has been secretly hurting herself and risking her safety. Her crewmates have noticed that she is preoccupied, depressed, and uninterested in her duties. She is not inspired by Voyager's latest adventure.
When one of the ship's probes is lost on a gas giant, Tom Paris takes the opportunity to suggest a new shuttlecraft he has been thinking of building. With a strong, fast shuttle equipped with the right technology they could fly into the dense gaseous planet and retrieve the probe. The shuttle would be very useful on many future missions. Tom has it all planned out. He has already worked out a design for the shuttle and calculated the amount of time and resources they would need. He has even given it a name: the Delta Flyer. When he presents his proposal, the crew is impressed and everyone agrees to begin collaborating on its construction.
B'Elanna, though, is strangely unenthusiastic about the new project. She submits designs for the hull composition and propulsion system, but does not seem to care much what comes of them. When Tom asks what's going on with her she withdraws from him. She spends her time running dangerous programs on the holodeck with the safety protocols off, gets hurt, and hides her injuries. She does make a gesture to reach out once, visiting Neelix in the mess hall after hours and having her favorite comfort food, banana pancakes, but she cannot bring herself to actually talk to him.
Meanwhile, the crew of a Malon ship has threatened Voyager and is attempting to steal the probe stuck in the gas giant. Seven of Nine scans the Malon ship and finds that the Malon are busy constructing a specialized shuttlecraft, just as the Voyager crew are doing. The Delta Flyer project goes into high gear, the crew determined to get it running and retrieve their probe before the Malon reach it.
They are almost ready to go, with just one last structural problem to work out. B'Elanna decides to find out how dangerous a problem it is. She simulates the new shuttle on the holodeck, complete with structural flaws, and takes it for a test flight... with the safeties off. The Flyer has a rough ride and B'Elanna is severely injured. In sickbay the Doctor patches her up, but on examination finds that she has sustained extensive, recent injuries. He informs Captain Janeway, who looks into the matter, searching through B'Elanna's holodeck logs and discovering that she has been risking her life. She takes B'Elanna aside and asks why she has been hurting herself. B'Elanna refuses to talk and Janeway relieves her of duty. She directs Tom and Chakotay to find out what is going on.
B'Elanna is discharged to her quarters by the Doctor, who has diagnosed her with clinical depression. Chakotay comes for a visit, and drags her to the holodeck, insisting she show him what she has been up to. He pulls up a program of hers - a war-ravaged cave filled with the bodies of their Maquis friends, their "adopted family." Chakotay begins to see what's going on. A short time ago, when Voyager received the first few data streams of letters from home, Chakotay and B'Elanna learned that the Maquis band they belonged to had been slaughtered by the Cardassians and their new allies, the Dominion (a rare mention of problems at home). B'Elanna has been unable to cope with this trauma. She has been unable to feel grief, sorrow, or real anger, and that disturbs her. When Chakotay asks if she is trying to commit suicide, she explains "I'm not trying to kill myself. I'm trying to see if I'm still alive." He promises to help his friend deal with this.
Finally, it is time to test the Flyer. The Malon have launched their new vessel. Seven, Tom Paris, and Harry Kim board the Flyer and get ready to leave. They are joined by a last-minute volunteer. B'Elanna insists she needs to be there to monitor the stability of the shuttle as it travels through the turbulent gas giant, and Chakotay allows her to go.
They race the Malon shuttle down to the probe, grab it, and begin ascending. The Delta Flyer's hull is strained to its limit. A rupture forms and B'Elanna quickly rigs up a force field with assorted equipment on hand. The shuttle survives, thanks to her. She celebrates with a big plate of banana pancakes.