I hated that Carter killed them
Reading some very old threads, it seems that it was Fox' decision to cancel the series due to low ratings.
That may be true, but it was surely Carter that decided to kill them and I often wonder if it was out of spite with Fox, or a way of saying FU to the fans who didn't show up, ironically, by taking it out on the fans who DID show up.
He could have brought them back into the X-Files fold but chose not to.
Sidebar: There was a report a year ago or so, that Carter was working on an animated X-Files series, but I've heard nothing since. Anyone?