You mean after Pagan Rome joined with the separatist church and Rome provided the newly formed Catholic church with it's vast armies???
The Christians (the universal church) who refused to join with Pagan Rome and the emerging Catholic church were branded as heretics and murdered as well...
Most of these heretical Christians were known as Arians. They never disappeared. In the seventh century one of them emerged as a charismatic leader, and since then these former 'heretical christians' have been known as Muslims.