The main starship classes from all three Star Trek (1966) spin-offs appear in the final shot of the episode. A Galaxy-class starship (the Enterprise-D from Star Trek: The Next Generation (1987)), a Defiant-class starship (the Defiant from Star Trek: Deep Space Nine (1993)), and of course an Intrepid-class starship (the Voyager from this series).
The producers considered ending the series with Voyager and its crew still stranded in the Delta Quadrant, since the crew had already started to perceive Voyager as their real home over the past seasons. This idea was ultimately scrapped.
Seven of Nine (Jeri Ryan) was originally going to die in the final episode; giving in to her romantic feelings for Chakotay would finally cause a fatal malfunction in her cortical implant. This idea was eventually abandoned.
In the Future scenes, Admiral Janeway visits Chakotay's tombstone before she leaves on her mission. According to the tombstone, Chakotay was born in the year 2329 and died in the year 2394 - the same year in which the USS Voyager originally returned to Earth from the Delta Quadrant.
This episode is chronologically the latest Star Trek episode to appear on television, with the exception of previous episodes and certain episodes in Enterprise that show events taking place after in the far future.
The first time a hypo-spray is administered to a location other than the neck of a patient. The Doctor applies it to B'elanna's stomach, presumably to apply it to the unborn (but soon-to-be-born) fetus.
47 Reference: GR 5-47432 is shown in the upper left corner of the comm display after Captain Janeway takes the device from the Klingons and is speaking with Korath, and again later when Harry contacts her.
The trivia items below may give away important plot points.
Although dealt a crippling blow, it is unclear if the Borg have been defeated once and for all, as the pathogen may not have had enough time to spread (Michael Okuda claims in the Star Trek: First Contact Special Edition DVD that they weren't). Chronologically, though, this episode marks the final appearance of the Borg, although they went on to make an appearance on ENT: "Regeneration".
Endgame" includes the ninth and final time Janeway "dies" in the series. On this occasion, her older self dies after infecting the Borg Queen with the neurolytic pathogen, and consequently destroying the Borg Unicomplex. The events of this episode also represent the tenth time (aside from the series premiere) that the Voyager crew has a possibility of returning home, but is the only attempt that proves successful.