In [#98 In The Flesh], the Delta Flyer is used as transport between Voyager and the Species 8472 terrasphere which contains a re-creation of Starfleet Headquarters.

Voyager has spent weeks tracking Federation signatures, only to find they emanate from a vast spaceborne structure inside which is a faithful re-creation of Starfleet Headquarters on Earth. Chakotay and Tuvok beam there from the Delta Flyer to investigate. When they beam back they bring with them an unconscious security guard, one of the participants in the simulation. The prisoner commits suicide when he realises he is on board a real Federation starship. The Doctor manages to make the body revert to its real form - a member of Species 8472 (pictured).

As Seven works to arm Voyager's photon torpedo warheads with Borg nanoprobes, Chakotay, Paris and Kim take the Delta Flyer back to the Earth simulation so that Chakotay can keep a planned date with the member of Species 8472 who is masquerading as Valerie Archer - it is an undercover mission and Chakotay's aim is to find out more about the Species 8472 mission against the United Federation of Planets. (The screenshot shows Kim and Paris waiting for Chakotay on the Delta Flyer.) However, Chakotay is unmasked and captured. When Paris and Kim notify Janeway that they have lost contact with Chakotay, she sets Voyager on a course to rendezvous with the Delta Flyer at the terrasphere. There she sets up a peace conference with representatives of Species 8472 from the terrasphere, Chakotay is released, and a truce is agreed.