In [#145 The Haunting Of Deck 12], the Delta Flyer leaves Voyager along with all other shuttlecraft when Janeway orders the crew to abandon ship.

As power is shut down on Voyager and the ship left in darkness, Neelix tries to keep the Borg children from being frightened by telling the story of the last nebula the ship travelled through. The children decide it must have something to do with the "ghost" that is said to haunt a sealed off section of deck 12. In Neelix's story an electric lifeform comes aboard Voyager, disrupting ship's systems. It communicates with Janeway by manifesting itself as the voice of the ship's computer. The lifeform is angry because the nebula it came from is no longer there and commands the Voyager crew to abandon ship. All the escape pods, all the shuttlecraft including the Delta Flyer are accordingly launched as all the crew except Janeway leave. (The departure is not seen on tv.) Janeway persuades the lifeform she can take it to a new nebula if it returns control of the ship. The creature agrees and releases Janeway. It takes almost two days for all the crew (and hence the escape pods and the shuttlecraft including the Delta Flyer) to return to Voyager, after which they seal off section 42 of deck 12, making it off limits to all but senior officers with a level-6 security clearance. In that isolated section they create an artifical environment for the alien lifeform during its transport to its new home. When a loud thud is heard, Neelix explains to the Borg children that it is the alien being released into the new nebula. When the children are frightened the lifeform is still aboard and will attack them, Neelix says he invented the story. But on the bridge, Janeway confirms that the lifeform is now safely outside, happy in its new home.