By 1999, Connor has become the supervisor of a scientific team headed by Dr. Allan Neyman (Allan Rich), which is attempting to create an electromagnetic shield to cover the planet, and protect it from the Sun’s radiation. The team succeeds, in effect giving Earth an artificial ozone layer. MacLeod and Neyman are proud to have saved humanity, and believe they will be remembered for a thousand years.
Unfortunately, the shield has the side effect of condemning the planet to a state of constant night. By 2024, the years of darkness have caused humanity to lose hope and fall into a decline. The Shield has fallen under the control of the Shield Corporation. The corporation’s current chief executive, David Blake (John C. McGinley), is focused on profit, and is imposing fees for the corporation’s services. A number of terrorist groups have begun trying to take down the Shield, among them Louise Marcus (Virginia Madsen), a former employee of the Shield Corporation.
Meanwhile, Connor MacLeod, now a frail old man, expects to eventually die of natural causes. As he watches a performance of Wagner’s Götterdämmerung, an image of Juan Sanchez Villa-Lobos Ramirez (Sean Connery) appears, and induces MacLeod to recall a forgotten event of his past. Five hundred years earlier, on the planet Zeist, a last meeting is held between the members of a rebellion against the rule of General Katana (Michael Ironside). The rebellion’s leader, Ramirez, chooses "a man of great destiny" from among them, MacLeod, to carry out a mission against Katana. At this moment, Katana and his troops attack, crushing the rebellion. Katana orders his men to capture Ramirez and MacLeod alive, and kill the rest of the rebels. The two captives are put on trial by Zeist’s priests, who sentence them to be exiled and reborn on Earth as Immortals in pursuit of "The Prize." Winning the Prize gives the victor the choice to either grow old and die on Earth, or to return to Zeist. Katana is unsatisfied with their decision, but the sentence is executed, leading to the events of the original 1986 film.
Back on Earth of 2024, Louise Marcus discovers that the ozone layer has in fact restored itself naturally, which means that the Shield is no longer needed. The Shield Corporation is aware of this development, but has chosen to hide it from the general public, in order to maintain its main source of profit. Meanwhile, on Zeist, General Katana decides that Connor cannot be allowed to return to Zeist, and sends his Immortal henchmen Corda (Pete Antico) and Reno (Peter Bucossi) to Earth to kill him.
Louise manages to reach Connor first, and asks for his help in taking down the Shield. To Louise’s disappointment, she finds the passionate person she once admired has grown into a tired old man. MacLeod explains to Louise that he is dying, and expresses his disapproval of terrorism. Before Connor and Louise can finish their conversation, Corda and Reno attack. MacLeod decapitates them both, regaining his youthful appearance by absorbing their energy during the Quickening. In the process, Connor summons Ramirez back to life.
In Glencoe, Scotland — the location of his death in the first Highlander film — Ramirez is revived. He finds himself on a theatrical stage during a performance of William Shakespeare’s Hamlet. Meanwhile, Connor has found a new lover in Louise Marcus. He attempts unsuccessfully to explain to her the concepts of his immortality. Elsewhere, General Katana arrives in New York, the scene of The Gathering and begins wreaking havoc.
Both Ramirez and Katana soon adapt to their new environment. Ramirez’s earrings are apparently valuable enough to pay both for the new suit he acquires from the finest and oldest tailor’s shop in Scotland, and for an airplane ticket to New York City. Katana finds New York much to his liking. After entertaining himself for a while, Katana manages to locate his old enemy, but their first encounter in centuries proves to be indecisive.
Soon thereafter, Connor is contacted by Ramirez. The latter joins MacLeod and Louise in their plan to take down the Shield. Katana, expecting this, forges an uneasy alliance with David Blake. The conflict between the two sets of allies eventually leads to the deaths of Dr. Allan Neyman, Ramirez, David Blake and General Katana himself. MacLeod succeeds in taking down the Shield by using the combined energies of his final Quickening from General Katana. Louise sees the stars for the first time in her life. Connor then claims The Prize by returning to Zeist with Louise. (Note: in the theatrical and DVD versions, both remain on Earth.)
Other new sequences include a battle between MacLeod and Katana atop a moving vehicle after they escape the security facility, and MacLeod and Louise climbing through a mountain tunnel to emerge above the Shield to confirm that the radiation levels are back to normal. The new version also removes a major continuity gaffe from the theatrical version, which had merged two separate swordfights between MacLeod and Katana into one longer climactic battle. The first sequence has MacLeod and Katana fighting in a large abandoned building about halfway through the movie (with MacLeod using a short sword), and the climactic swordfight takes place much later (with MacLeod using his original katana). Since the two sequences are merged, Connor’s sword changes for no apparent reason. The director’s cut version restores them to two separate battles, although it never shows how or when Connor reacquired his katana. The gaffe wherein Katana's sword changes from his giant "spring loaded" broadsword, to the smaller broadsword used by the two punks still exists in the final battle of both versions.
Still not completely satisfied, producers William Panzer and Peter Davis decided to revisit Highlander II once again in 2004. Dubbed the Special Edition, this cut was nearly identical to the Renegade Version, but with a few alterations. The most obvious change is the introduction of new CGI special effects throughout the film, including a now-blue shield as originally intended. Other significant changes include a small piece of voiceover work by Lambert and the inexplicable removal of a short scene near the end of the film in which Louise Marcus holds off a group of TSC guards with a gun. Shots of a crashed space ship where the Zeistian rebels meet in secret 500 years ago is altered so that it appears "A Very Long Time Ago" some rebels meet at an old stone fortress. However, modern looking firearms are still seen briefly in some of the desert battle sequences, as well as the use of explosives and gas masks.
Some time after the 2004 version was released, a handful of fans took scenes from all three officially-released versions, as well as the deleted scenes, and edited together a fourth version of the film that runs nearly two hours, and contains all of the new Director's Cut footage, but retained the Zeist aspect. In addition to the Director's Cut footage and deleted scenes, they also took the so-called "Fairytale Ending," and incorporated it into the ending of the film.
This ending is sometimes seen in televised broadcasts of Highlander II: The Quickening. The VHS version simply cuts off after Connor looks up at the starry sky and smiles, after the smoke from the explosion of the December Installation clears.
Critics and audiences alike pointed out that the characters suffered from a lack of motivation; an example often offered is that no reason was provided for Katana’s sudden interest in Connor after apparently losing contact with him for 506 years, and his insistence on killing his old enemy while he could wait for him to die without outside interference. Also, the two “alien” Immortal protagonists on Zeist have their Scottish and Spanish names that they will have on Earth. They were acquainted with each other on Zeist, but the transport process must have erased their memories. Thus Connor never learns about his true past until he senses the voice of Ramirez, decades after winning the Prize, and he is forced to recall the events of the distant past. This caused confusion for many viewers, even those who had seen the first film. The movie even contradicts itself in places. For example, when Katana sends Corda and Reno to earth wanting MacLeod killed even though he has won the prize, is mortal now and has chosen not to return to Zeist. Later, after they fail he arrives on Earth and tells MacLeod that he is not going back to Zeist, MacLeod replies that he never intended to, but Katana knew this earlier and still sent Corda and Reno anyway.
According to the documentary Highlander II: Seduced by Argentina, the film’s apparent poor performance is partially result of the bonding company’s interference with the work of director Russell Mulcahy, as well as economic problems within Argentina itself, the location the movie was filmed. Mulcahy reportedly hated the final product so much he walked out of the film’s world premiere after viewing its first 15 minutes. For similar reasons, Christopher Lambert threatened to walk out of the project when it was nearing fruition, but he didn’t, due to contract obligation.
Among critics, Roger Ebert of the Chicago Sun-Times gave the film a score of one half star (out of four), saying: "Highlander II: The Quickening is the most hilariously incomprehensible movie I've seen in many a long day—a movie almost awesome in its badness. Wherever science fiction fans gather, in decades and generations to come, this film will be remembered in hushed tones as one of the immortal low points of the genre. Giving the film a score of 2 out of 10, IGN's review of the film said: "How bad is this movie? Well, imagine if Ed Wood were alive today, and someone gave him a multi-million dollar budget. See his imagination running rampant, bringing in aliens from outer space with immensely powerful firearms, immortals who bring each other back to life by calling out their names, epic duels on flying skateboards, and a blatant disregard for anything logical or previously established—now you are starting to get closer to the vision of Highlander II.
Awarding the film one star out of five, Christopher Null of FilmCritic.com said, "Highlander has become a bit of a joke, and here's where the joke started. [...] Incomprehensible doesn't even begin to explain it. This movie is the equivalent of the 'Hey, look over there!' gag. You look, and the guy you wanted to beat up has run away and hid. David Nusair of Reel Film Reviews gave the film two stars out of four, saying: "It's hard to imagine Highlander II appealing to non-fans of the franchise, as the film barely captures the sense of fun that was so prevalent in the original. With its complicated storyline and dreary visuals, it occasionally feels more perfunctory than anything else—though, to be fair, it's nowhere near as bad as it's been made out to be over the years.
Reactions to the updated versions of the film have been more positive. Reviewing the 2004 "Special Edition" DVD, David Ryan of DVD Verdict gave it a score of 69 out of 100 and said that "[this] is the best version of this film that [the producers] can make with the material they have on hand. It's still not a particularly good film—but it's infinitely superior to the original version. [...] What was once a horrible, horrible film has become downright tolerable, and actually somewhat entertaining at times.
When Ramirez is brought back from the dead, in the theatrical version of Highlander II, he comes back wielding a Scottish cutlass. Ramirez never shows surprise at being equipped with this blade. Only in the Directors' Cut/Renegade Version is it seen that Ramirez collects this sword from a stage set. Nevertheless, after 2,000 years of using a two-handed weapon, he adapts to the use of this single-handed weapon with ease. When he and MacLeod fight in MacLeod's apartment, neither he nor MacLeod comment on his sword. Nor does Ramirez inquire as to the wherabouts of Macleod's katana.
After setting off to destroy the Shield, Ramirez has his katana back, and ultimately plants it into the ground before stopping the giant fan from destroying MacLeod. MacLeod leaves both Ramirez and the katana behind. However, for the final battle with General Katana, he has his Japanese sword back again. Exactly how he retrieves this sword is never even hinted at. Apparently, originally, the sword was supposed to be magically returned to Macleod, but this scene was never filmed (see Production Notes section below).
A number of intentional similarities can be seen between the first three films in the series: