In the classic X-Men comics, the Phoenix was originally portrayed as a secondary mutation for Jean Grey. It was later retconned as having been a cosmic entity. In the new movie X-Men: Apocalypse, it seems as if the Phoenix Force is portrayed as being a secondary mutation, with no evidence of any cosmic origin.
Which one do you like best, for find less confusing? The Phoenix as a secondary mutation, or as a cosmic entity bonded with Jean Grey?