This larger story arc "The Dark Phoenix Saga" is broken up into two parts. The first part is The Phoenix Saga in (X-Men #101-108). This is the second part of the two-part series mostly taking place in X-Men #129-138.
The Creation of the Dark Phoenix Saga
The Dark Phoenix Saga was created because of the number of fans that loved the original Phoenix Saga. Marvel needed a way to bring the Phoenix back in a way like never before, so they decided to have the Phoenix come back to earth evil. They figured what better way to shock the readers than to have the once great and powerful balance maker turn evil and show its true colors. This idea resulted in the creation of the Dark Phoenix Saga.
How it Started
After taking some time off to find herself, Jean Grey journeyed to Muir Island. While shopping she met a strange man named Jason Wyngarde, who was secretly the old X-men villain "Mastermind". After Mastermind toyed with Jean's mind, she decided to stay on Muir Island so that Moira MacTaggart could test the full extent of her new powers. During an emergency alarm concerning Moira's son Proteus, Jean was swept up in an illusion of herself in the 1800's as Lady Jean Grey (an ancestor of Jean's). Lady Jean Grey was the wife of the era's Jason Wyngarde and Black Queen of the Hellfire Club at that time. This psychic illusion caught her off guard and she was felled by Proteus. Later during the Proteus situation, Mastermind once again took Jean into his 19th Century illusion where he convinced her that a cruel game of manhunt was her own idea!
Following the defeat of Proteus Jean returned to the mansion and very quickly got reports of 2 new mutants, Kitty Pryde and Dazzler. The team decided it would be best to split up and look for the two mutants, Jean decided to search for Dazzler. When Jean researched Dazzler's last known location, she found that Dazzler worked at a nearby club so she decided to look there first. At the club where they find Dazzler was performing Jean once again saw Jason Wyngarde walking across the floor and was instantly brought back into the illusion where she was his wife. While in the illusion Cyclops's face appears and Jean is able to break free from it. While Jean walked out of the club, Jason sends Hellfire grunts after her and in little time, they are all defeated.
During the assault, Wyngarde brought Jean into one last illusion where she was the Black Queen and helped him along with the Inner Circle take down the X-men. After that she then and took her place as their new Black Queen.
Dark Phoenix Saga
Jean Grey's powers were increasing it began to corrupt her and make her want more and more energy which caused Jean to develop a split-personality. At first Jean was able to control it but as time went on it became harder and harder to control. Mastermind wanted to join the Hellfire Club and captured Jean Grey by using her hunger to his advantage. Mastermind made Jean think she was in the 18th century by using hallucinations and in time, she became the “Black Queen”.
In attempt to save Jean, the X-Men were captured and chained up in the corner of the dining room. When the Hellfire Club was sitting at the table for supper Emma Frost saw Jean’s puzzled face and soon realized what was going on. She knew that Cyclops was trying to connect to Jean Grey through their telepathic connection (which only Scott and Jean shared). Emma ordered that Mastermind do something at once. Mastermind then had a telepathic battle with Cyclops inside of Jean Grey’s mind and in the end Mastermind killed Cyclops, making the real Jean Grey heartbroken. Jean reassumed control over her body and powers for a short amount of time but when the Phoenix retook control of her body she became overwhelmed with madness. The Phoenix broke free of Mastermind's illusion. Confused and angry the Dark Phoenix turned itself into a bird-like form of pure fire, and stated “No one can control the power of the Phoenix!" and burst through the ceiling and flew to the roof. Mastermind followed her to the roof in hopes that he would still be able to control her, but soon learned that he was no match for the mighty Phoenix.
When the Phoenix was done with Mastermind, Cyclops got to the roof and called out Jean Grey’s name. That upset the Dark Phoenix so much that she broke out and yelled, “The mortal Jean Grey is no more, I am the Dark Phoenix!". The Phoenix then felt Jean Grey retake her body once again (only for a few seconds) but manages to say the words, "Scott, Help Me". When the Dark Phoenix retook control, she shot a fire ball at them which blew the X-Men into a nearby park.
The Dark Phoenix then flew over to the park and told the X-Men that their destinies had come to an end and that the Dark Phoenix had come to destroy them all. Then the battle began and in the end, the X-Men lost. Cyclops (being the last to go down) was hit the hardest because he had upset the Dark Phoenix the most, mainly because he confused her. When the Dark Phoenix asked Cyclops why he had cared about the body of Jean Grey so much, he replied, “I love her”. That statement made the Dark Phoenix upset because she didn’t understand or know what the emotion felt like, so she replied, “I do not understand, your answer is unacceptable” and used a force-field to wipe him out. When Cyclops was knocked out Jean Grey retook control of her body again (this time for a longer period of time) and walked over to Cyclops’s body and started to cry.
She then said, “Don’t ever forget Scott, I will always love you.” The Dark Phoenix resumed control and became madder than ever and took the form of an enormous bird made out of pure fire. This figure was seen for hundreds and hundreds of miles. The Dark Phoenix then flew straight up into the sky until she was no longer seen. The waves of power that the Dark Phoenix gave off when she transformed into the birdlike shape were sensed by extremely powerful telepaths throughout the universe, each one showed an extremely puzzled face.
The Dark Phoenix then entered space and created a black hole to teleport into another galaxy (D’Bari Galaxy). The Dark Phoenix dove into the D’Bari’s star and started to feed on its energy until there was nothing left but a nova.
When the Shi’ar tried to attack the Dark Phoenix she then turned around and attacked back, but with little effort, luckily not destroying the Shi’ar but causing more than enough to damage to give them the hint to back off. The Dark Phoenix then flew back to earth causing the captain in charge of the spacecraft to contact the empress and give her the warning. Meanwhile when all of this was going on, Beast was creating a machine that would neutralize the power of the Dark Phoenix, but only for an extremely short period of time. Once created Beast tried to figure out where the Dark Phoenix could be headed next but had no trouble figuring it out.
Beast along with all the other X-Men (including Xavier) went to Jean Grey’s childhood home and waited for her to arrive. When she arrived Xavier tried to fool the Dark Phoenix by putting hallucinations into her head, making her think that her parents are sitting in the drive way waiting for her. Once Jean walked outside, the car started to pull away causing Jean to go farther and farther into the yard as she chased after it. When she was far enough, the X-Men made their move and with some luck Beast slipped the device onto Dark Phoenix’s head. At first it looked like it was working, the Dark Phoenix had fallen to the ground in pain, but after a few short seconds the Phoenix stood up and melted the device. The Dark Phoenix then became overwhelmed with rage, she laughed and taunted Beast for his failure. Dark Phoenix picked up the X-Men with her telekinetic powers, by this time it looked like the X-Men had finally came to their end, but then out of nowhere Xavier tries his best to invade the mind of the Dark Phoenix and successes. He then summoned the Dark Phoenix to a telepathic battle.
Dark Phoenix knows that Xavier is no match for her, so she decides to taunt and play around a little bit. He tries his best to defeat her, but once the Dark Phoenix had had enough she then decided to destroy him. She had almost succeeded, but Xavier called for the help of Jean Grey herself (who is in a way trapped within her own body) just in time. Together with the two extremely powerful telepaths working together, they are able to bind the Dark Phoenix into her own powers, but only for the time being.
Since the Dark Phoenix had been contained, Jean Grey was able to retake control of her body once again. Once she awoke, Jean Grey was greeted home by all her fellow X-Men. It seemed like everything had just fallen back into place. Then the Shi’ar arrived and tried to take Jean Grey away so that they could destroy her and the evil, powerful creature that was within her to ensure the universe’s safety. The empress then ordered her Imperial Guards to capture Jean. The X-Men got ready for the battle of their lives and were willing to do anything to protect Jean. Luckily for them Xavier was able to enter the mind of the empress and found out that if the Imperial Guards were challenged to a battle, they must accept it. The X-Men were then brought onto the spacecraft and were taken into space. On board, Jean Grey was accused of genocide and the only solution was death. The X-Men and the Shi’ar agreed that there would be a battle and the winner would determine Jean Grey’s fate. Once the X-Men had gotten ready they along with the Imperial Guards were then teleported to a moon where the battle would take place.
The X-Men (not knowing they were no match for the Imperial Guards) then decided to split up into pairs. After many hours of battle Jean Grey and Scott Summers were the last two left in the match. Before the two decided to give the Imperial Guards the best they had, Jean and Scott hid in a nearby cave to say their last few words before they fought for their lives. When they were done they ran out and were confronted by all of the Imperial Guards. Jean and Scott were doing great until Scott was shot down. The sight of Jean Grey’s true love falling to the ground put so much guilt and stress on her that the Dark Phoenix was able to retake control of the body once again. By doing so she sent off extremely powerful waves of power which knock off the energy flow of the Shi’ar spacecraft.
The Dark Phoenix then went after the Imperial Guards and had them feel the wraith of the Dark Phoenix. Once the Imperial Guards were out of the picture Jean Grey had retaken control of the powers and body. She knew that her control over the Dark Phoenix was not going to last long and right under the Shi’ar spacecraft. She then used her powers to boost the spacecraft’s weapon system. Thinking that the Shi’ar’s weapon was powerful enough to kill her and the Dark Phoenix she said her farewell to Scott by saying, “I love you Scott, don’t ever forget, I will always be with you.” The empress blasted the weapon directly at the Dark Phoenix. During the blast the Dark Phoenix had retaken control of the body forming once again the shape of the fire bird, then it was gone.
Thinking that the Phoenix was destroyed, the empress then teleported herself and Xavier to the moon. She apologized to Scott along with the other X-Men. Then out of nowhere the Phoenix rose from her ashes as the Phoenix Force and brought Jean Grey’s body with her. The Phoenix then apologized to all the X-Men. She explained to them how she lost her way and assured them all that it would never happen again. When Scott asked what would happen to Jean, the Phoenix Force told him that the flame within her was no more, but that with a small portion from many would be enough to restore the life within Jean Grey. The X-Men accepted the deal and they all grouped together and watched as a small part of each of them went into Jean Grey. The Phoenix then said, “I have been here too long, I must depart” and flew away. When Jean woke up, the first thing she said was Scott’s name and the saga ended with Jean Grey kissing Scott Summers.