Many things were changed from the original comics when the Phoenix Saga and Dark Phoenix Saga were adapted into the film Dark Phoenix. This is par for the course whenever a classic written work is adapted for a visual medium and even with an extensive X-Men cinematic universe having been established by earlier movies, there was no way to include every aspect of the original storyline in a single film.
The character of the Phoenix was first introduced in Uncanny X-Men #101, after the apparent death of Jean Grey while trying to guide a spaceship through a manual reentry into Earth's atmosphere. The Phoenix Saga ran through Uncanny X-Men #108 and established how Jean had formed a connection with the Phoenix - a cosmic being tied to the power of creation itself. The Dark Phoenix Saga began with Uncanny X-Men #129 and detailed how the efforts of the villainous Hellfire Club to corrupt Jean Grey served to give the Phoenix a taste for destruction, ultimately leading to the death of 5 billion innocents. The saga ended in Uncanny X-Men #138 with Jean's funeral, after she sacrificed herself to deny the Phoenix Force a host.
While Dark Phoenix broadly follows the plot of the original comics, the fine details have been drastically altered. Jean Grey is still empowered following a trip into space and gives up her life to save the universe, but what happens in between those two points is an entirely different story. Here is everything Dark Phoenix changed from the original comics and the reasons why those changes were made.
The X-Men Roster Is Different
The most obvious cosmetic change between the comics and the movie is that there are two entirely different rosters of mutant heroes. The team in Dark Phoenix is made up of Jean Grey, Cyclops, Storm, Nightcrawler, Quicksilver, Beast, Mystique and Professor X. The X-Men team at the start of the Phoenix Saga consists of Jean Grey, Cyclops, Storm, Nightcrawler, Colossus, Wolverine, Banshee and Professor X. By the time of the Dark Phoenix Saga, Banshee had left the team and the X-Men are assisted by Kitty Pryde, Dazzler, Angel and Beast over the course of the ten-issue storyline.
There are a variety of reasons why Dark Phoenix utilizes the team that it does. The chief one is so that the team matches the line-up that we saw at the end of X-Men: Apocalypse. Another factor is that several of the characters involved in the Dark Phoenix Saga of the comics aren't around at the time of Dark Phoenix in the X-Men movies' timeline. Banshee, for instance, was established as having died sometime before the events of X-Men: Days of Future Past in 1973 and Wolverine would not join the team until sometime in the late 1990s.
The Movie Has A More Compact Timeline
Another major change is how long the story of Jean Grey's cosmic empowerment lasts. The events of Dark Phoenix take place over the course of several days, with Jean seemingly transforming from Phoenix to Dark Phoenix after a single day. By contrast, the story of Jean's metamorphosis in the original comics was told over the course of three years and saw Jean functioning as the Phoenix with her new powers for a considerable length of time. It seems a safe bet that this was changed for reasons of pacing, in order to tell a more action-driven story.
There Is A Different Reason Why The X-Men Go Into Space
In Dark Phoenix, the X-Men are sent into space at the request of the President of the United States, in order to rescue a team of astronauts whose shuttle has lost radio contact with NASA. The original Phoenix Saga saw the heroes heading into space for a much more personal cause. With the assistance of their ally, astronaut Dr. Peter Corbeau, the X-Men infiltrated a Space Shuttle launch in order to storm the space-station hideout of Dr. Stephen Lang. An anti-mutant bigot, Dr. Lang was attempting to secretly relaunch the American government's Sentinel program, which used specialized robots to hunt and kill mutants.
There are two main reasons why this aspect of the story was changed for the movie. The first is that the Sentinels were already used as the chief menace of X-Men: Days of Future Past and bringing them back would distract from the story of Dark Phoenix. The second is that the President calling the X-Men into action effectively establishes them as publicly-known heroes, who are no longer fighting to defend a world that hates and fears them - a marked contrast from earlier movies in the franchise.
No Shi'Ar Empire or Lilandra In The Movie
In the original Phoenix Saga, the nature of the Phoenix Force is explained to the X-Men by an alien woman named Lilandra, whom Professor X had been having visions of for some time before she finally arrived on Earth seeking shelter from the followers of her brother, Emperor D'Ken of the Shi'ar Empire. The Phoenix Saga ended with Jean using her connection to the Phoenix Force to stop the insane D'Ken's efforts at utilizing an artifact called the M'Kraan Crystal to attain infinite cosmic power. The story ended with Lilandra becoming Empress and Jean having achieved a rapport with the intelligence behind the Phoenix Force.
There were rumors at one time that Angeline Jolie would be playing Lilandra in Dark Phoenix. Ultimately the character would not be included in the final script and the duty of explaining the Phoenix Force to Jean Grey (and the audience) would be handed over to Vuk of the D'Bari. Played by Jessica Chastain, the character of Vuk acted as a composite of various alien characters from the Phoenix Saga and Dark Phoenix Saga, including Lilandra, in order to minimize the cast and keep the story of Dark Phoenix moving.
No Hellfire Club or Mastermind In The Movie
In the original Dark Phoenix Saga, the corruption of the Phoenix comes about because of the machinations of the Hellfire Club. Led by an Inner Circle of wealthy mutants, the Club saw the X-Men as a threat to their power-base and enacted a plan to take control of Jean Grey. This task was overseen by Jason Wyngarde (aka Mastermind), whose mutant power to create convincing illusions allowed him to slowly seduce Jean with fantasy images of another life where she was an 18th Century noblewoman engaged to the dashing Lord Wyngarde. This unknowingly fed the Phoenix with an increasing desire for more decadent delights, eventually leading to Jean's transformation into the Dark Phoenix.
The Hellfire Club and most of the relevant members of the Inner Circle were already already introduced into the X-Men movie universe in X-Men: First Class. However, most fans were not pleased with their portrayal there and writer/director Simon Kinberg said that he could only introduce the Hellfire Club in Dark Phoenix if he "had four hours to tell this story." As with Lilandra and the Shi'ar, the task of pushing Jean to stop repressing herself and feed the Phoenix fell to Vuk of the D'Bari.
Wolverine Had A Major Role In The Comics
It's no surprise that Wolverine had a major part to play in both the Phoenix Saga and Dark Phoenix Saga, given his popularity at the time the original comics were published. Many of Logan's fans consider Uncanny X-Men #133, in which Wolverine fights a one-man war through the Hellfire Club's headquarters to save his teammates, to be one of the greatest Wolverine stories of all time. Unfortunately, there was no way to recreate this classic scene on the big screen, due to the absence of the Hellfire Club and Hugh Jackman's retirement in the role of Wolverine. Even if Jackman had been persuaded to return for one more go, Logan's presence in the story wouldn't have made sense in the cinematic universe's timeline.
Beast Has A Larger Role In The Movie, Yet Does Less
Hank "Beast" McCoy has a major role in Dark Phoenix, being the first person to turn on Jean after the Dark Phoenix takes over and the one who brings Magneto into play by telling him that Jean killed Mystique. Strangely enough, Beast didn't show up in the original comics storyline until close to the end, due to his being a member of the Avengers at the time instead of the X-Men. Despite this, Beast played a major role in the battle against the Dark Phoenix, building a device that hindered Jean's ability to think clearly. This bought Professor X and Cyclops the time they needed to get through to Jean and get her to fight back against the Phoenix Force. We do not see this in Dark Phoenix, however, due to the changes in the movie's climax.
The Comics Show More Of The Marvel Universe
Another major change in the story of Dark Phoenix is that we don't see any of the Marvel Universe at large reacting to the events of the story. For instance, the Dark Phoenix Saga features a scene where Empress Lilandra confers with the leaders of other alien empires, including the Empress of the Skrulls and the Supreme Intelligence of the Kree, regarding how to handle the Dark Phoenix. Chalk this one up to both Fox not having the rights to use as many alien races as you'd think (despite their owning the film rights to the Fantastic Four catalog) and the changes to the final battle during reshoots.
The Final Battle Is On Earth Rather Than The Moon
Much has been said about how the climax of Dark Phoenix was changed from a battle in outer-space to a fight on a moving military train. The original ending would have been more in keeping with the spirit of the original comics, where the X-Men faced the Shi'ar Imperial Guard in a trial by combat in the Blue Area of Earth's moon to determine whether or not Jean Grey should be executed for the actions of the Phoenix. Presumably the D'Bari would have filled the role of the Shi'ar Imperial Guard had the original ending to Dark Phoenix been utilized.
Xavier Retires Instead Of Cyclops Quitting The Team
Dark Phoenix ends with Professor X retiring, Beast taking over running his school for mutant children and the school being renamed in Jean Grey's honor. In the original comics, the Dark Phoenix Saga ended with Cyclops quitting the team and Professor X resuming his role as the team's leader while welcoming his first new student in some time, Kitty Pryde. Presumably the ending was changed to better fit Professor X's character arc over the course of the movie and set up the final scene in which he is approached by Magneto, who offers him a home in his island commune and a friendly game of chess.