In [#110 Dark Frontier, Part 2], the Delta Flyer travels to Unimatrix One to rescue Seven from the Borg Queen.

Following Seven's capture by the Borg during Voyager's covert mission aboard a Borg sphere to steal a Borg transwarp coil (seen in Part 1 of the story), Janeway leads an away team in the Delta Flyer to find Seven.

Voyager shuttle maintenance crew modify the Delta Flyer for flight in transwarp space
the same footage is used in [#97 Extreme Risk] and [#110 Dark Frontier, Part 2]

the Delta Flyer launches; the same footage of the Delta Flyer leaving the shuttlebay is
used in [#97 Extreme Risk] and [#110 Dark Frontier, Part 2]

They use the stolen transwarp coil to take the Delta Flyer into transwarp space. The Delta Flyer has now been installed with multi-adaptive shielding, which is technology designed to hide them from the Borg and which is based on the field notes of Seven's parents during the research they conducted from aboard their ship the Raven.

Meanwhile, Seven has been taken to the Borg Queen's lair. The Borg plan to use her knowledge to assimilate humankind.

view of the huge Borg spaceborne complex, which includes the Borg Queen's lair,
as seen through the front window of the Delta Flyer

Janeway sends a message to Seven through her Borg interplexing beacon but the Borg Queen discovers it as it comes through. As the Borg adapt to the Delta Flyer's multi-adaptive shielding, Janeway is forced to beam into Unimatrix One in an attempt to disable the shield matrix around the Borg Queen's chamber. Janeway confronts the Borg Queen and orders Seven to leave with her. The Borg's dispersal field around the chamber blocks the Delta Flyer's transporter beam, but Seven tells the Janeway to fire her phaser rifle at the power node above the chamber. This disrupts the Borg Queen's command interface, and Janeway and Seven are beamed to the Delta Flyer.

The Delta Flyer flees into a transwarp conduit, pursued by a Borg vessel.

the Delta Flyer in a Borg transwarp conduit

On Voyager, Chakotay and Torres fire a full spread of photon torpedoes at the threshold of the transwarp conduit threshold, collapsing it just as the Delta Flyer exits. The Borg ship is destroyed.