Ten years before the present-day events of the film, Kell orchestrates the death of Connor's adopted daughter Rachel Ellenstein. Heartbroken, Connor departs for The Sanctuary, where Immortals are under surveillance by a subgroup of Watchers to prevent The Prize from being won.
A decade later, Kell and his disciples attack the Sanctuary, and Connor is believed to be beheaded along with the other Immortals there. Duncan MacLeod (Adrian Paul), compelled by a vision, begins to investigate and nearly dies at the hands of Kell and his minions. Later, he discovers Connor was spared by Kell, so as to allow the evil Immortal to make his life even more miserable. Kell wants to kill Duncan in order to torture Connor, and given the number of Quickenings he has received, this seems quite likely to occur. Additionally, Connor is too guilt-ridden by the deaths of all his loved ones to stand up to Kell by himself. Therefore, Connor forces Duncan to kill him, allowing Duncan to absorb all of Connor's power in order to defeat Kell.
Amongst Kell's followers is Duncan's Immortal wife Kate, a woman whom he wedded in 1713 and "killed" on their wedding night in order for her to become Immortal. This has driven her into the arms of Kell, and he must earn her forgiveness, or face her as an embittered part of Kell's faction.
Ultimately, after Kell executes his group in a mock Last Supper to gain their powers, Duncan and Kell have a final battle. At first Kell easily overpowers Duncan even when Duncan attempts a supposedly unbeatable move that Connor taught him. At the last moment, Connor seems to take control of Duncan's body and kills Kell by jumping over him and decapitating him as he turns around and is too slow to avoid the strike. Duncan absorbs all of Kell's massive power. He then goes to Glenfinnan, Scotland to bury Connor with his wife Heather. The Producers' Cut ends with the revelation that Kate is still alive.
The film features several shots from the original Highlander. The first is a computer-altered and enhanced shot of Glenfinnan, which was originally the shot of Connor walking away from his village. The second is a shot of the Silvercup sign, pulled from the scene of the Kurgan taking Brenda to the building. And in the rooftop Quickening, two shots of Connor and Heather together are also taken from the first film. Castle Stalker is seen briefly in the film during Connor's flashback scene. This building was also seen in Monty Python and the Holy Grail.
Donnie Yen served as the film's martial arts choreographer and also played the role of Jin Ke, who was based a real historical figure: Jing Ke, renowned for his failed assassination of the Chinese emperor Qin Shi Huang. Professional wrestler Adam Copeland, known as "Edge" in the World Wrestling Entertainment, makes a cameo appearance as Lachlan. A reference is made to Copeland's wrestling persona when Duncan says to Lachlan, "Looks like you've lost your edge, lad."
Endgame's theatrical distributor, Dimension Films, demanded that cuts be made to the film to give it a faster pace. The deleted footage contained exposition necessary to understanding the Highlander universe, resulting in a theatrical cut that was criticized for being incomprehensible to audiences unfamiliar with the franchise. An extended cut with restored footage was later released on DVD. (See "alternate versions" below.)
The Region 1 (United States and Canada) DVD includes, as a bonus feature, a rough workprint cut of the film. The visual quality of the rough cut is rather poor, with unfinished special effects and a timecode visible at all times, and alternating between widescreen and full-screen. This cut features a subplot involving Connor giving a Christmas tree to an orphanage every Christmas, an activity picked up by Duncan after Connor's death. Kate does not appear in this version of the film at its conclusion, unlike the producers' cut included on the DVD.
An unauthorized fan edit exists titled Highlander Endgame: Connor Lives Version. In this version, Connor snaps out of his depression and confronts Kell for a final duel to the death. A surprised and enraged Kell loses his head to the newly invigorated Connor Macleod, as an injured Duncan observes. In this version, the time line was restructured so the present day of Endgame can occur before the present-day events of the first Highlander film. Clips of New York City were added to show it as it appeared in the early 1980s compared to the cleaner, modern version of 2000. As the film closes, Connor warns Duncan to watch his back as the time of the Gathering approaches. A shot of Duncan fades to black as his ultimate fate remains unknown.
Elvis Mitchell of The New York Times gave Endgame a mildly positive review, saying: "It's nice to see mindless violence back in a B picture, where it belongs, and the swordplay is impressive. When [the movie] sticks to the hand-to-hand battles and doesn't try to offer deeper thoughts on the life of an immortal, it works on its own terms. IGN gave Endgame a score of 8 out of 10, saying that "fans will be pleased," adding: "Endgame proves to be both true to the spirit of the first film and the television series, [it has] a solid story to tell, [and it] features the best fight sequences of the series."
Andrew O'Hehir of Salon.com said, "Personally, I enjoyed it about the way I enjoyed the Mortal Kombat movies, meaning that its genuine fun and its unintentionally ridiculous moments are roughly in balance. Lisa Schwarzbaum of Entertainment Weekly remarked: [Fans] will be thrilled that Connor MacLeod and his fellow clansman Duncan MacLeod engage in a vein-popping showdown to see which immortal will bump off the other, thereby achieving a quickening of multiorgasmic proportions. Those who aren't in the cult of this popular genre fantasy not only won't understand what the previous sentence is about, but may also wonder what's so great about perpetual life if it entails shlepping from one badly lit, cheesily art-directed, peat bog-colored century to another, spouting hollow dialogue."
Travis Eddings of Film Threat gave the film one half star out of five, saying: "After viewing Highlander: Endgame, it's obvious that Aarniokoski has no idea how to make a film. [...] The only reason why this film earns one-half of a star instead of zero is due to some unintended laughs. It's funny to see what passes as acting in this movie. James Brundage of FilmCritic.com gave the film one and half stars out of five, saying: "Highlander: Endgame possesses all of the elements of a straight-to-video action movie. Cheap special effects that look cool, weak characters that still pull heartstrings, and a bunch of actors no one really knows unless you have seen this or that obscure flick. And, taking that view, one wonders why the hell I even had to watch Highlander: Endgame in theatres.
Carlo Cavagna of About Film called the film "a disaster," adding: "The plot and the characters' motivations are nonsense. Lambert's character has nowhere to go, and his once-magnetic glower is tired and worn. Several opportunities for spectacular action are squandered because the movie's villain has a tendency to execute summarily his own henchmen. Paul's modicum of charisma, director Douglas Aarniokoski's broad panoramas that recall the original Highlander, and Lambert's amusing skirmishes with a Scottish accent are not enough to provide any redeeming value.