Xavier's dark side is the part of him that would use his powers for personal gain and conquest...the "Mr. Hyde" to Xavier's "Jekyll." Xavier consciously kept his dark side under control at all times.
Shortly after Moira MacTaggert's arrival at Xavier's School, she gave him a sedative to help him with the severe psychic distress he was suffering due to his initial psychic contact with Lilandra (though at the time he knew not the source). With Xavier's psychic defenses weakened, his dark-side gained freedom. It generated psychic constructs of four of the original X-Men (Angel, Beast, Iceman, Marvel Girl) and sent them to attack the "new" X-Men (Banshee, Nightcrawler, Storm, Wolverine) while they trained in the Danger Room under Cyclops (the sole remaining original X-Man at the time). These constructs derided the newcomers and Cyclops alike and even attempted to destroy them, but Cyclops and Wolverine eventually realized that they were fighting illusions.
Having recovered partially, the real Xavier crawled into the Danger Room, resisting the sedatives with all of his will, and caused the false X-Men to vanish. "Dark Xavier" then appeared, mocking and threatening to kill them. The X-Men's physical assaults against his psychic form were of no avail, and they began to fall before his illusions. However, the real Xavier then caused the illusionary X-Men to reappear under his control and to attack "Dark Xavier." Begging for mercy, Dark Xavier swiftly fell back under the real Xavier's control and vanished. Nonetheless the real Xavier wondered if he were going mad.
Xavier's dark side developed a life of its own.
Initially, Xavier's conscience held his dark aspect in check—he could only act during Xavier's deepest sleep, when his psychic defenses were at their weakest. As the dark aspect grew stronger, it began manipulating Xavier—the more Xavier slept, the more powerful the dark aspect became. The more powerful the dark aspect became, the more Xavier slept.
While Xavier slept, the Entity could steal his power, doubling its own.
Xavier's dark self, now known only as the Entity, somehow penetrated the Spacewall, appearing in the Microverse in the outer fringes near the Spacewall. He swiftly devastated a number of the "frontier worlds."
The Entity was, however, unable to manifest in the Earth-616 dimension.
The Entity wrested worlds from Baron Karza's control practically effortlessly. Karza's armies were decimated while attempting to oppose the Entity.
The Entity conquered and enslaved the D'arnellians, a race of farmers, turning them into soldiers in his army. Mortified by the Entity, the D'arnellians swiftly constructed an immense battle fleet.
Learning of the onslaught in the fringe worlds, the Micronauts investigated the region. Recognizing the immensity and evil of the power they were up against, they teamed up with their enemy, Baron Karza, to oppose it.
The Micronauts (Acroyear, Bioship, Bug, Fireflyte, Huntarr, Marionette, Arcturus Rann), alongside Karza's fleet encountered and battled the D'arnellian fleet. Both D'arnellians and Dog Soldiers rapidly died by the thousands in the savage struggle. Karza and Bioship were held in reserve in case the Micronauts failed, and Bioship's sensors determined that the power they faced originated from Earth. From an asteroid, the Entity himself confronted the warring armies. Rann asked him why he waged war against the Microverse, and the Entity replied "For the fun of it!" as he snapped his fingers and shattered the planet D'arnell. Bioship shielded itself and Karza from the flying planetary debris, while the Entity bound the Micronauts against asteroids. The Entity then sensed the presence of Bioship and Karza, and they fled at full speed to escape his wrath.
Karza and Bioship arrived on Earth (their sensors tracing the power source to Xavier), with Karza emerging first in the X-Men's Danger Room where he quickly overpowered the New Mutants. The X-Men (Ariel, Colossus, Nightcrawler, Storm, Wolverine) faced him next, and when Kitty tried to phase through Karza, their minds were transferred into each others' bodies (though none of the others realized this, and Karza's psychic shields prevented its discovery). Maintaining control of both Kitty's and his own form (via telepathy), Karza—joined by Bioship—told the X-Men of the Entity. Professor X sent the X-Men to accompany Karza and Bioship back to the Microverse to aid against the Entity.
Xavier's efforts to psychically locate the Entity failed. Exhausted, he fell asleep.
Via illusions and mind games, the Entity bent the Micronauts to his will. He suffered a moment's agony when Xavier was briefly roused by a commotion caused by the New Mutants, but regained his power as Xavier fell back to sleep. Vowing to stop the cause of such agony, the Entity remade the Micronauts in costumes matching those of the original X-Men.
Karza dispatched his true body to the Body Banks, while Bioship brought the X-Men towards the Entity (via his psychic link to Rann), As they began to land, the Entity shut down Bioship completely, causing him to—relatively gently—crash. The X-Men emerged to find themselves tiny beings in a replica of Xavier's estate. Entering, they encountered "Xavier" and his new "X-Men" (the Micronauts). After welcoming the real X-Men to "Professor Xavier's Alternate School for Gifted Youngsters," "Xavier" sent the Micronauts after the real X-Men; upon the Micronauts victory, "Xavier" revealed himself as the Entity.
While the real Xavier slept (sleep enforced by the Entity), the Entity-controlled X-Men and Micronauts slaughtered one of Karza's Dog Soldiers' asteroid outposts (Kennels). Xavier felt the death of each Dog Soldier. When Huntarr stopped the Karza-possessed Kitty from slaying their prisoners, the Entity arrived and criticized their mercy. When Rann tried to argue for the prisoners, the Entity disintegrated and then re-formed him to prove his power. The Entity then slew each of the remaining Dog Soldiers himself. The Entity confronted Karza's recorder, the Archivist, allowing it to continue transmitting data to Karza as he obliterated the entire Kennel. The Entity teleported himself and his slaves away at the last second.
The X-Men and Micronauts were thrown into a dungeon between missions, though the Entity was impressed with Kitty's (Karza's) cruelty and kept her in his palace. He began to put the moves on her.
Via contact with a concerned Dani Moonstar, the real Xavier loosed his psychic self and sent it to confront the Entity who loosed his own psychic self and met with Xavier on the psychic plane. Sensing the Entity's weakness Karza/Kitty stole the Entity's knife and stabbed him through the back. Weakened by the assault, the Entity seemed to fall before Xavier's assault. When Xavier unmasked the Entity, he was stunned to see his own face, and he was even more shocked as his form changed into that of the Entity, and vice-versa. Now it was the real Xavier bound in the Entity's psychic bonds.
With Xavier's defeat, the Entity now gained access to his body on Earth-616, which he took over.
The Entity-possessed Xavier psychically caressed Moonstar's soul, filling her with waves of pleasure and bending her to his will. Meanwhile, the X-Men and Karza, having broken free of the Entity's will and escaped their dungeon, discovered the Entity's dying form, now housing the true Xavier's mind. Xavier revealed the mind-swap b/t Kitty and Karza. Bioship's equipment helped keep the Entity's body alive.
The Entity accessed Cerebro, plotting to amplify his own abilities to destroy entire systems within the Microverse. The Enigma Force felt pain as a blast from the Entity pierced the Spacewall and obliterated some of the uninhabited frontier worlds at the Microverse's outer fringes. Karza's battlefleet was obliterated as well, and chief scientist DeGrayde was among those who died. Bioship (housing the Micronauts, X-Men, and the Xavier-possessed Entity) narrowly avoided being destroyed as it breached the Spacewall and traveled to Earth. No sooner had they arrived when the Entity-controlled New Mutants (Cannonball, Magma, Spellbinder, Sunspot, Wolfsbane) attacked them, and both the X-Men and Micronauts were left at relative disadvantage as they were only a few inches tall.
Xavier had the X-Men fight to provide a distraction for the Entity and had Nightcrawler keep the Entity's body alive until he instructed otherwise. Xavier sent his psychic self to approach the Entity, secretly entering his mind. The Entity took control of Karza's Kitty-possessed form, forcing it to assault Kitty's Karza-possessed form, which could not phase to safety. The two regained their own forms with the aid of Fireflyte, and Karza teleported away, while Xavier began attempting to perform a psychic lobotomy to excise the Entity from his mind. During the battle with the New Mutants, Nightcrawler had been forced to take the Entity's body and flee Bioship, and the body died without the needed life support.
Having detected Xavier's presence, the Entity sent his own psychic self to confront him, but Xavier—who had taken control of his own body's autonomic functions while the Entity had been distracted by the battles—caused the illusion of a fatal stroke. Fearing death or being trapped within a mindless body, the Entity fled Xavier's form and returned to its own. As that form was dead, it apparently ceased to exist.