Trivia: Boothby (or other members of species 8472) should not know about the provisional rank insignia worn by former Maquis members. When Chakotay is there making his survey, he risks being discovered.
Trivia: Unbeknownst to Voyager, an invasion of shape shifting aliens from outside the Alpha Quadrant had already infiltrated Starfleet Headquarters two years previously: The Founders from the Gamma Quadrant's Dominion. This was shown in the ST: Deep Space Nine episodes "Homefront (1)" and "Paradise Lost (2)".
Nitpick: When Voyager first approaches the station, Captain Janeway orders Tuvok to charge weapons. Then, a few moments later, Seven reports that the station is charging weapons, to which Janeway replies, "Do the same."
Nitpick: Chakotay mentions he left Starfleet in 2368 to join the Maquis; however, according to the Deep Space Nine two-part episode "The Maquis", they didn't form until 2370. It's possible that there was a precursor organization that was later incorporated into the Maquis a few years later, however.
Trivia: Directive 010: "Before engaging alien species in battle, any and all attempts to make first contact, and achieve non-military resolution must be made."
Trivia: This episode marks the second time that a simulation features Ferengi officers in Starfleet. The first is The Next Generation's "Future Imperfect".
Kim: I've always wondered what it would be like to date an alien.
Chakotay: I'll take notes.
The Doctor: (when the human "Ensign" reverts to his natural Species 8472 form) Talk about a wolf in sheep's clothing.
8472 Boothby: There's a drone sitting at this very table. Look at her; all gussied up to make her look like a human being.
Seven: I am no longer part of the Collective.
8472 Boothby: Once a Borg... always a Borg.
8472 Boothby: Targ manure! 'United Federation of Planets'... 'tolerance for all species'... the 'Prime Directive'... targ manure, every word of it!
Tuvok: Your metaphor is colorful but inaccurate.
8472 Boothby: Vulcan logic; add that to the list.
8472 Boothby: Captain Janeway.
Janeway: (sarcastically) Mr. Boothby. Nice to see you. Enjoying the Delta Quadrant?
8472 Boothby: Don't get sassy with me, young lady! This recreation may be Starfleet but our weapons are far more sophisticated. I can destroy your vessel with a single command. Run along, now.
Janeway: I'm not going anywhere; not until you return my First Officer and give me a damn good explanation for what you're doing in our galaxy!
(Kim is pacing around the shuttle)
Paris: Take it easy, Harry, we didn't build the Delta Flyer to withstand such extensive pacing.
8472 Bullock: Enough! We must not negotiate with these creatures!
8472 Boothby: Sit down, Admiral.
8472 Bullock: (surprised) Sir?
8472 Boothby: I said sit down, or I'll knock you right on your human butt!
Ray Walston (Boothby) is credited as a special guest star.
Janeway: Just be home before midnight!
This is a reference to Cinderella, in which a young maid attends a ball but must be home by midnight, when her horse and carriage will revert back to a pumpkin and mice.