In [#146 Unimatrix Zero, Part 1], the Delta Flyer is destroyed by the Borg.

Seven awakens from her regeneration cycle disturbed that she dreamed a beautiful forest with trees and flowers and a man who called her by her given name, Annika. Back in her alcove, Seven retires again, this time wearing a cortical monitor the Doctor gave her to monitor her REM sleep. Upon closing her eyes, she immediately finds herself back in the beautiful forest (pictured; screenshot is from Part 2 of the story). She meets the man whose name is Axum, and he explains that they are in Unimatrix Zero, a cyberhaven where drones revert to their pre-Borg individual personalities, but it is experienced only by certain drones who possess a recessive gene and they lose all memory of Unimatrix Zero when their regeneration cycle ends. They ask for Voyager's help. The Borg Queen is aware of them and is trying to track them down.

the Delta Flyer in the shuttlebay

With the discovery of the existence of Unimatrix Zero, Janeway's plan, which is ultimately only partially realised (in Part 2 of the story), is to start a Borg civil war in which the drones will regain their independence, with drones who have the recessive gene retaining their memories and hence their individuality when they wake from their regeneration cycles. As part of the plan, Voyager attacks a Borg class-4 tactical cube while Janeway, Tuvok, and Torres take in the Delta Flyer. They have been injected with Axum's nanovirus, modified by the Doctor to nullify the cortical inhibitors of the mutated drones so they will retain their memories of Unimatrix Zero once they leave their alcoves. The plan is to spread the virus throughout the Borg Collective by releasing it into the central plexus of the class-4 tactical cube, because the central plexus is the Borg unit which links Borg ships. The Borg Queen destroys the Delta Flyer moments after the away team beams onto the Borg cube.

destruction of the Delta Flyer

the Delta Flyer is destroyed (pop-up window)

It is noted that the starboard plasma injectors on the Delta Flyer tended to run a little hot at high impulse and the warp matrix was out of alignment by .3 microns.