Thousands of years ago, when man was still young, and sorcerers, sorceresses, witches, and warlocks were just discovering their abilities in the magical arts, a powerful witch (Aithne (Irish meaning fire)), yearning for immortality both summoned a Goddess of the Ancient Religion (Bandia Fola (Irish meaning blood goddess)) and fused her soul with its essence creating the Vampires.
Thousands of years later, by the time of Merlin's birth, Vampires were all but extinct and the Dark Mother (Original) was in hibernation beneath Camelot (in the dragon's cave). When the threat of Morgana and Mordred came to its peak (seasons 4 - 5), the Dark Mother called to Merlin and, as she herself died, she granted him her gifts, fusing the Goddess' essence with him instead of her and tethering it to his soul making him the Dark Father (I'm going to say season 4) and the new Original.
As Gawain lay dying, Merlin Turned him and the Vampires were resurrected from extinction. Years later (this is an AU where Gawain lives (obviously), Lancelot lives, and Arthur lives) with Guinevere marrying Lancelot, Arthur admits his love for Merlin while Merlin reveals his status as a Warlock and the Dark Father, magic is allowed and returns to Albion; Arthur asks Merlin to allow him to join him in eternity, Merlin Turns Arthur, Merlin's magic allows him to fall pregnant with him as the "mother" and the father being Arthur (obviously). All but one of their many children elect to remain Human (they ARE mortal but are stronger and faster than other Humans allowing them to be the perfect Royals and defenders of Albion).
Centuries later, in a possible epilogue, Merlin is in his flat gazing over the streets of modern London (2015) reminiscing over his past when he feels a pair of strong arms wrap around his waist and himself pulled into a broad, muscular chest and he and his mate of these past few centuries (Arthur) share a chaste, loving kiss when Arthur lowers a hand to rub over Merlin's now noticeable baby bump.