The X-Men had a similar history as their mainstream counterparts, until the time-traveling Brotherhood, posing as the original X-Men, arrived and created a divergent reality.
When those past X-Men took over the evil megacorporation Alchemax, they used it to hunt and persecute Mutants for unknown reasons, including the X-Men of 2099.
When they were trying to steal medicinals to help the people who lived in the so-called Outlands, they encountered another X-Men team from the past.
Together, they fought Alchemax's private police, the Public Eye, as well as the Onslaught Sentinel, until the young X-Men traveled back in time again trying to return to their home reality.
Links and References