Okay, I know it's very long and very detailed. But you can change it.
Basic idea is this;
Merlin is trained in İsle of Blessed in his entire life with Morgause. And their teacher is Nimueh. They becames best at both magic and non-magical tecniques. Then They became High Priest and Priestess. Merlin goes to Camelot. Morgana felt a connection to him and attracted to him. Then a danger arrises and Morgause sends to Camelot for help him.
Apprentice of Nimueh:
Starting at 8 years before series 1. 10 years old Merlin. Nimueh is not evil. She believes prophecy of Emrys. One day Merlin loses control of his Magic. Druids offer their help. They explain Hunith, the boy is Emrys, so he needs to learn magic from very powerful sorcerers. The druids take him to İsle of Blessed, where the centre of Priestess of Old Religion lives. Nimueh takes Merlin as her Apprentice. He trains with Morgause. Nimueh calls Alator the Catha for train Merlin in torture and resistance area. Merlin and Morgause becomes best friends. Merlin gets used to calls as Emrys. Both Merlin and Morgause trained as High Priest and Priestess.
9 year later, Nimueh and other priestess decided to send Emrys to Camelot, for fulfil his Destiny. Emrys and Morgause goes to Ealdor. Merlin gets used to call his own name again. They both finest at sword fighting and Magic.
1 year later Merlin goes to Camelot. He saves Gaius in his first day in Camelot. He doesn't tell Gaius he was trained by Priestess, and he became a High Priestess. He saves Arthur's life and became his manservant.
One month later a most powerful High Priestess leaves Priestess of Old Religion and declares war to Camelot (Not Nimueh, someone else). Merlin one day will be most powerful warlock. But he is not strong enough to defeat her alone. Priestess sends Morgause to Camelot for help Merlin. Morgause comes Camelot in a Knight Armour. She wants to became a Knight of Camelot. She challenges Arthur and wins. Then she takes off her helmet. And Arthur becomes outrageous. Because he lost to a girl and promised to Knight a girl to Camelot Army. Uther have to knight her as a Knight of Camelot.
But Gaius recognise her and fears for Priestess of Old Religions plans for Camelot. He thinks the High Priestess that declared war, still works under the commands of Priestess and Morgause is a spy. He tells Uther, Morgana's sister Morgause still alive and in Camelot. Uther wants to execute her but Gaius convinced Uther to wait and learn her motives. Because a High Priestess is too dangerous.
( Merlin/Morgana) , ( Morgause/Leon) , (eventual Arthur/Gwen )