Though John had only met Merlin a couple of times as opposed to how many times he had met Mycroft, he did find the young man quite charming and utterly unlike either of his brothers. Sure Merlin was just as brilliant as either of them but Merlin was by far more social-able and likable then either of his brothers. Somehow Merlin had come out of his childhood able to interact with people just like everyone else. Which was so utterly unlike either of his brothers that John was baffled by how the three of them could be related. He knew that they were, they looked far to much alike to contemplate anything else but it was amazing. What was more amazing was the fact that when John had met Merlin he had been married.
John remembered when he had met Merlin's husband, Charles. Sherlock would later say that John could have been shot and he still wouldn't have reacted as all John had done was stare at Charles in mere idea of a Holmes brother being married was truly insane and thus all John could do was just stare in shock at Merlin and Charles. The fact that Charles was an aggorant git made John want to hit him and take Merlin far from him as Merlin was to kind hearted and genuine to be around anyone that could harm him. Of course that would entitle keeping him far away from his brothers and John was not suicidal.
Before meeting Merlin, John had though that Mycroft was overprotective of Sherlock but after meeting Merlin and seeing how his elder brothers reacted around him, John learned the true meaning of over protectiveness. The elder Holmes brothers knew every moment of Merlin's day. Sherlock had an entire part of his underground network following his brother and John would not be surprised if Mycroft had an entire section of the government that watched Merlin every single second of the day. John was truly amazed by how well the young man coped with it. John had asked him once how he dealt with it and Merlin had just shrugged, and said:
"I know they do it out of love and I do the same...Just because my protection isn't so obvious or invasive doesn't mean it isn't there. I will always look after my brothers for as long as I am around."
John didn't know what that meant but didn't doubt the brothers love for each other. It was proven beyond a doubt when Merlin left Charles and while John still didn't know what had happened in their marriage, he did know that Mycroft kidnapped Charles to find out what he had done to Merlin. While Sherlock had his network searching every single dealt of Charles life. Neither Sherlock or Mycroft let Merlin find out but John knew by the way Merlin was around more often that he was aware of it and was just humoring them. Merlin would not speak of Charles again and would soon begin dating the suddenly outed Prince Arthur. John had no idea how any of it came about but was happy for Merlin.
Though dealing with Sherlock had not been fun for months after that, for all Sherlock did while not on a case was obsess over Arthur and trying to find something wrong with him. So that Sherlock could get him away from his brother and whenever John would point out that Arthur was making Merlin happy, Sherlock would roll his eyes.
"Charles made Merlin happy and yet Merlin left him and will not tell either Myrcoft or myself what he had done. Arthur will do something as well so all I am trying to do is tell Merlin now before he gets to close and gets hurt again. Merlin was with Charles for three years, seven months, one week and three days. If I find out what is wrong with Arthur now, it will be much more efficient for my brother. No wasted time."
"Perhaps there is nothing wrong with the Prince. He is the future King of this country. There are entire media sites dedicated to him, Sherlock. If there was something wrong with him, then it would be known."
"Those sites aren't me and those sites aren't brother to Merlin...Those wretched sites have been writing about Merlin, questioning when ,...Well, Mycroft has taken care of several of those so called writers already."
John winced and had stopped questioning Sherlock as he could only imagine what Mycroft had done to the press as some of the papers had almost come out and called Merlin a slut and gold digger. Among other things and John had been furious at them all and he was nowhere near as protective of Merlin as his brothers were. Eventually things had calmed down and Sherlock would resign himself to Arthur just as he had Charles or so John assumed. Moriarty began to take more of Sherlock's time, especially after Moriarty threatened Merlin. Never had John seen Sherlock so frantic and worried over something before and it was then that John began to truly worry that his friend would use again.
Something that Mycroft and Merlin also worried about as they had both basically moved in with them, along with the security that was now around Merlin at every single moment, security from both Mycroft and Arthur. Showing that Merlin had added yet another protective person in his life. Making John feel even sorrier for Merlin as now he had three people trying to control his life.
The months that followed were not easy for anyone and then Sherlock was framed as a fraud and killed himself, leaving John bereft of everything. Merlin and Mycroft seemingly disappeared from his life and John only heard about Merlin marrying Arthur on the TV. Just as he heard that the first heir to the British throne to be artificial created was born to Arthur and the Holmes cousin, Freya. William Henry George Sherlock Pendragon.
John would not see Merlin again until his life was turned upside down again by the arrival of an alive Sherlock.