The mad Shi'ar Emperor D'ken hoped to use the Crystal to gain ultimate power when the nine "death-stars" aligned, but in the end, he was stopped and driven completely mad. During the battle to stop D'ken, the X-Men were transported inside the Crystal, along with some of the Imperial Guard. The conflict continued until a deflected beam hit the center of the Crystal and cracked the neutron galaxy's container. Phoenix II merged with the galaxy and managed to fix the bubble, saving the universe.

Years later, new fluctuations in the Crystal signaled the beginning of a wave that crystallized the entire universe. The X-Men figured out that the Crystal was reformatting the universe because the past had been changed by Legion, but although Cable's astral form was sent back to warn the four X-Men who had been taken with Legion, the past was still changed when Legion accidentally killed his father, Charles Xavier.

The M'Kraan Crystal changed reality into the "Age of Apocalypse," although Bishop, already a man out of his time, was left in place. Twenty years after that pivotal event, in what passed for the present in that reality, Bishop found the X-Men and told them that they had to undo the damage done in the past. Teams split up on different missions, one of which was to bring back a shard of the M'Kraan Crystal, through which they could open up a doorway to the past. The shard was eventually captured by Apocalypse and regrown into a complete crystal. In that reality's final battle, Nate Grey plunged the original shard into Holocaust's body, transporting them to our reality. Dark Beast and the Sugarman both ended up inside the full crystal, and came to our reality twenty years in our past. Bishop, Illyana, and Destiny also went into the Crystal, where Illyana tapped into one of herselves form another reality, where her mutant powers had already manifested, and generated a stepping disk that sent Bishop to stop Legion and negate that whole timeline, restoring our own.

However, other realities exist in which the Age of Apocalypse remained the de facto timeline. In the maintained AOA, humans and mutants worked together to rebuild Earth, and the M'Kraan Crystal was placed in a secure facility with a nuclear bomb failsafe. Interestingly, the reconstituted U.S. Army maintained the facility, yet they did not know the purpose and function of the crystal, though Magneto was the new Director of Mutant Affairs and technically part of the government. The facility was later infiltrated by Holocaust, returned to his birth reality by the Timebroker. Holocaust slaughtered the base personnel and took control of the crystal. His purpose is still unclear, though it seems he wants to confront the Timebroker and free himself and all the Exiles.

When people crossed over to our reality from the Age of Apocalypse, including X-Man, the Crystal sent its guardians Modt and Jahf to destroy them, as they didn't belong in our world. X-Man managed to defeat them, and they left the other corssovers alone.

Recently, a connection has been theorized between the M'Kraan Crystal and the Exiles' Tallus, though the exact details are unknown.