Disclaimer: I do not own the idea that Merlin went to Hogwarts (that's J.K. Rowling's), and I also do not own Merlin (that's BBC's).
A/N: So, this is the background story to my two other stories, "the Origin of Merlin's Horn", which is being revised as of now, and "A Witch's Quest of Mount Doom", which next chapter is being worked on. This story could also be read separately as my attempt to bridge J.K. Rowling's statement in Pottermore, which mentioned that Merlin enrolled in Hogwarts, with BBC's Merlin, and those two with the actual legend. Enjoy!
In truth, Merlin was deeply annoyed. He was not his great-great-great-great-great-grandfather, anyway. Despite being named after the old man, he was not the inventor of wand magic. But what could he say? That blasted finding had set the whole wizarding community abuzz that time, and ever since, they totally bugged him about it. At first, it was just his friends teasing him. Then, some people thought he was the reincarnation of his ancestor. It was bloody annoying when people revered him for things he didn't even do.
And now, in the afterlife, it still bugged him. People now confused his deeds with his ancestor's. Come on! He couldn't be the Court Sorcerer of King Arthur if he was born hundreds of years after the said king's time. That was what the other Merlin did. Although he had heard rumours in the afterlife that his ancestor was never a court sorcerer. Instead, he was a servant to the king. Which was of course a preposterous idea! (He refused to believe that the greatest wizard in history was a servant, even though the spirit who told him was the spirit of one of the closest knights to King Arthur. What was his name again? Gaw... Gwa? Oh, Gwaine. Sir Gwaine. He insisted on being called sir.)
Then he couldn't possibly be the inventor of wand magic. Master Slytherin and the other Founders of Hogwarts taught him that. Please. Just check the record of the school. Everyone could find his name written in the list of students.
He would let people say anything about founding the Order of Merlin, or helped saving Narnia, or assisted 13 Dwarfs took back their home along with a Hobbit and an Istar, as his great deeds. But please, please stop thinking he was 'the Great Merlin Emrys of Camelot'. As he had said before. It was BLOODY ANNOYING.
Oh how he missed the time before they found out who the inventor of wand magic was.
In truth, Merlin didn't care about what people think of him. Many people may 'worshipped' him for inventing wand magic, or revered him as the greatest wizard in history, or confused his deeds with those of his great-great-great-great-great-grandson. All he cared about was waiting for the Once and Future King to rise again. And maybe some family things.
After he sent Arthur to Avalon, he returned to Camelot and reassumed the position of servant. In his free time, he invented a kind of magic that was easier to learn. He called it wand magic. Other people, though, called it New Magic, to differenciate it from the Old Magic. He taught many people of wand magic. They might not remember who taught them, since after they mastered it, they taught it to others, and so on, and so on. But Merlin never searched for any recognitions. He was only glad that magic flourished, in the form of the Old Magic, or the New Magic.
He married, eventually. His wife was a lovely Druid girl with warm brown eyes and bushy locks as dark as his own. And he had children he named after the most important people in his life who had departed. There were little Balinor, little Arthur, little Gwaine, little Ana, and little Freya. At first Merlin wanted to name his daughter after Morgana, to remind him of how kind the woman was before she was twisted with evil, but considering how bad her reputation was, he named her just Ana instead.
Camelot prospered, under the rule of the gentle but firm Queen Guinevere. After she removed the ban of magic, everyone lived in peace. Gwen offered him the position of Court Sorcerer, but he refused. "I was a servant to Arthur, and I will always be," was the exact words he said to Gwen at the time. But soon everything came to an end. Gaius died, then Leon, Gwen, Percival, his wife, his sons, and finally, his daughters. And he was still the same.
With grief, he gave his goodbye to his grandchildren and disappeared from the world, hiding. He watched over his grandchildren, of course, and their children after them, and their children, and so on, but he didn't intervere much. He just made sure they were fine and capable to live their lives.
Among his great-great-...-grandchildren, there were two that stood out of the others. The first one was named after himself. He lived an ordinary life, until a journal of his that he had carelessly forgotten to take when he was moving for like, the hundredth time in his life was found by the next occupant of the house. The journal was mostly about how he discovered wand magic. After that, people started to investigate and finally found out about his life and his discoveries. Well, it was actually more like they guessed about his life from the fragments of his life he wrote in the journal and then compared them to the entries written by a 'Geoffrey of Monmouth'. Merlin was not sure if the Geoffrey who wrote those entries were the same Geoffrey who were the librarian of Camelot. It was more like this persona was stealing Geoffrey's name. His entries were inaccurate in many parts, and when combined with the uncomplete and rather random notes from Merlin's journal, resulted in a very inaccurate legend. For an example, Mordred was not Arthur and Morgana's son! Whoever started the idea was really sick. They were siblings! Another example, he was never a Court Sorcerer. And whose idea was it to call Elyan: Sir Elyan the White. Poor Elyan must be suffering a lot of teasing for that in Avalon.
Back to the topic, after the finding, people started to demand things from this other Merlin, and since then, his life changed. It was not entirely bad for him. In the end, he even travelled between time and space to save people. It was pity that his son was more like his otherworldly mother in ability than his father. His son had no magic, but was really strong and beautiful.
The second was a very brave woman. Her name was Hermione. She reminded Merlin a lot of his wife with the warm brown eyes and bushy hair. She helped brought down a dark wizard and like the other Merlin, she travelled to another world to help people. When she travelled though, she didn't know that her destiny lied in that other world.
Merlin stretched his bones. He always hated his 80-year-old-man disguise. His body ached all over. But then again, he kind of needed the disguise. He observed that people tend to ignore him when he was a grumpy old man, and he didn't want to be recognised this time. It was not the time, not yet. There will come a time when he won't need to disguise himself again, when the Once and Future King once again ruled Albion in peace and prosperity. But this was not the time. Soon, he will rise again. And then, Merlin Emrys would again stand by his side as his servant and friend. Soon.
A/N: Sorry, I forgot to put line breaks between the two sections. Even I was confused when I was re-reading this. :D