What if Morgana was called upon by her followers, they needed her guidance. Seeing as the Ministry of Magic began outlawing anything 'Dark' which even included the wizards and witches who followed the Old Ways- let alone one with dark magic. They needed their Dark Goddess back. She answers their pleas.
-Side note this will be a 'twisted' dark story. Also Grindelwald was terrorizing 1934 to his defeat in 1945. Yeah there was no time line really, I made my own and still working on it. I have a rough time line of Riddle's time in Hogwarts so some things will go off that not all.
Contrary to popular belief, Morgana was not evil, Goddess of War- yes; someone whom was killing because they could- no. Morgana magic did lean more toward the dark, but that meant nothing at the time, she still could do light spells with a little more practice- dark spells did not take as many tries. She was Goddess, once she was a human, a witch but human. She once believed that someone was her Soul-mate, but this was not true, he lied in order to prove she was a witch and kill her. She was hurt, angered, and betrayed- like anyone would be. Leaving, she went far away to learn how to use her powers to the fullest extent. She was going to get her revenge. In her time away she gathered followers and with those followers she found something she would have never thought. Peace. And a reason to not get revenge. She did not want to see her people hurt, with that thought and all the people who worshiped her brought her from the enchantress to the Goddess she is known for today.
Morgana, unlike Merlin who had a creature of magic teaching him (A DRAGON FOR CRYING OUT LOUD), learn that magic had no real limits. As long as she could think it could happen, with that being said: magic was a muscle. It was weak in the beginning, she had to work constantly to even get close to Merlin, and he was using it all the time. As the time went on she was able to not only get to Merlin's level, she went beyond. Morgana pushed herself to the limit, all to protect the people that slowly came to her.
Morgana became known as a magnificent leader. Soon people flocked to her, and in turn she healed them. Morgana could not turn them away- after all they were poor, and hurt because of Urien. Urien was killing all who opposed him or who he thought would. Soon her little home was surrounded by more homes, which lead to a bustling city. Once Morgana stared to have a following, she started teaching the children whom showed signs of magic. She showed them how to control the power they had, she showed them they did not need to be afraid of the power they held. They were the ones to stay in the castle she moved to the void and keep praying her, kept her strong while away. She soon became known as the War Goddess because she was ruthless when defending her home and her followers.
One thing she did not see was the fact when she left, she used her powers (What little she could use), Urien- the man she thought was her soul mate- rallied the whole town together. He also got Arthur and Merlin against her. Like her, Merlin, was able to use magic but because of the time they were in, he was not prosecuted. (After all he was male and on their side.) Morgana's spies, her ravens, Memoria (Memory) and Mens (Mind) - She got the idea from one of her followers that was from a distance land of ice. They told her of the coming legion, and who was leading it.
She was able to get her people to safety, there were a few to stay behind and help. Those were her most faithful. Once Urien and the legion got to her gates, Morgana and five followers awaited them. The two had a spat, were Arthur and Merlin saw who the real evil was but, it was too late. Morgana gathered her power and moved her fortress to an unknown location. A location where the rest of her people waited for her. She left her people there and wandered the world, learning all she could of magic. A few times she came across Merlin and when she did, they fought. Merlin's betrayal hurt her more than Urien ever had.
Morgana was killed by Merlin, yes that is true. But it was an accident, he was trying to ride a town of a dark creature, one that Morgana found out was not harming the town. A wizard was a pinning it on the poor Thestral. Morgana saved it but got kill in its place. Merlin was surprised, Morgana whom was dark saved an animal, when he went to her body it was gone along with the animal. The Thestral took her home, where she was given a beautiful send off. Her followers knew she would return to them. She did. She was reborn into the world whenever her followers call upon her. She had been reborn five times, then she meet him- which changed everything she was working for.