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Many people are convinced that Sherlock, and particular s3, is full of “no homo” moments, but apart from John repeatedly stating that he’s not gay, I fail to see the same attitude in Sherlock. Actually, there’s one thing I’m sure of after watching s3, namely that Sherlock is in love with John.
First of all, from the start of s1, Sherlock never denied or corrected assumptions about him being in a relationship with John. He might have been oblivious to what actually being implied, but it’s probably not the case. He never corrected those who assumed he was gay, even though we’ve seen him correcting people on almost everything else. He never defined himself as straight, either. In fact, he flat out stated that girlfriends are not really his area. On the other hand, he thought John was flirting with him, and told him that he was “flattered” but that he considered himself married to his work. (And that was really, really early in their relationship, so Sherlock’s caution is definitely understandable.)
In TBB, we get the idea that Sherlock sees his investigations with John as dates; because they go out and have fun together, and they like each other; Sherlock states that, it’s not something shippers came up with. So, it could be Sherlock being his usual weird self, or there could be more behind it. (It might be interesting that in TSOT, which is written by Thompson as well, Sherlock organises the stag night so that he and John are going to drink in the places where they found corpses…in a way this might strengthen the impression that Sherlock considers his adventures with John as dates that ought to be celebrated and remembered. Of course, he knows that with the wedding things are going to change…so, could the stag night be considered as a sort of farewell to their “happy” times together? Given the wistful ending of the episode I think this view might not be completely far-fetched.)
From TBB onwards (up until ASIB) we get Sherlock acting definitely not in the nicest possible way to John’s girlfriends. Is he annoyed that they’re getting in the way? Definitely, even though we also get the idea that John puts always Sherlock first (and that’s why his relationships don’t last long). Is Sherlock jealous of these women? I’d venture to say that yes, indeed, he is. Does he realize this? Maybe not. In ASIB we get Irene, and she does her best to make our detective flustered. Well, she manages to confound him, to impress him, but he doesn’t seem sexually interested in her. In the same episode we get Mycroft’s snide comment which seems to imply that Sherlock is actually a virgin. Surely, he doesn’t seem very comfortable around sex. (Something that pops up again in s3, by the way.) So, maybe he’s just not particularly interested in sex at all, which could be the case. On the other hand, in the same episode, Irene points out to John that he and Sherlock are indeed a couple, no matter what they say. She’s smart, she’s not fooled. She’s an expert in the field of attraction. John once again points out that he’s not gay. As for Sherlock…no answer. But Irene doesn’t seem to be his type, in spite of everything.
Irene is also important because she gives Sherlock the “final proof” that “love is a dangerous disadvantage”, something that could be, in a way, Sherlock’s cautionary motto for s3. We know that Sherlock considers himself to be “heartless”; he told as much to Moriarty, but we know that it’s not true, and probably Sherlock himself doesn’t believe that either. We know that Sherlock’s most powerful pressure point is John…we’ve known that from the start, and it’s something that remains as a constant throughout the series. Actually, it gets steadily more and more noticeable.
In s3 we get Sherlock kissing Molly…except that’s a fantasy. That’s Anderson’s fantasy. We also get a Sherlock fan imagining that Sherlock kissed Moriarty…much to Anderson’s outrage. But what do those scenarios have in common? Easy, they’re not real. Some people got angry because in this series Sherlock kissed lots of people, but not John. But that’s exactly the point. Sherlock kissed Molly, Moriarty and Janine. But the first two kisses were clearly not real, they didn’t actually happen, and the kisses to Janine were part of an act. So, not real. I don’t see those two het kisses as an instance of “no homo” because IMHO they’re actually reinforcing the idea that Sherlock kissing women is not real, not something he would do, and definitely not his idea of “fun” if you consider how quickly his mask slips when Janine gets out of the flat. Sherlock kisses Molly on the cheek, in TEH, and it’s after he has thanked her again for her help and after she has told him that she has found someone. It is a loving gesture, but it’s not sexual. It should also be added that in HLV it seems that Sherlock didn’t actually sleep with Janine, which is quite interesting in itself. Sherlock didn’t seem to care much about manipulating her, so why no sex? It could be that he’s not comfortable with it (which would be consistent with his reactions in other episodes) or he’s not that much into women. Or both.
On the other hand, in s3 Sherlock is very much shaken by the news of John’s impending wedding. As pointed out by many, at the beginning of TEH Sherlock’s bravado is mostly a façade to cover up his nervousness. (The façade is an important theme in s3, BTW.) Sherlock knew that John had got a very bad blow from the whole Fall thing…he knew because he had seen and heard him in the cemetery. But he didn’t know John had left Baker Street. He didn’t expect it, or he just hoped he would be still there. Sherlock is surprised when Mycroft tells him that John is not living there anymore and that he’s moved on. Sherlock has been away, but he had not moved on; he wanted to come back to John.
So, Sherlock takes the news of John’s relationship and impending wedding with outward aplomb, but it’s clear it’s something that is going to have a huge impact on his life. In TSOT Mrs Hudson underlines how much the marriage will change things. Sherlock pretends to be cool with it, saying that it’s not a big deal, but as soon as she’s out of the room we see him looking wistfully and longingly at John’s chair and then he walks to his own room, and mutters “Into battle” before picking up his suit for the wedding. If Sherlock were not worried and shaken by the whole issue all this wouldn’t make sense at all. Does this make sense if friendship is the only tie between Sherlock and John? I really don’t think so. End of an era, indeed.
Sherlock’s best man speech is basically a love letter to John. As others pointed out, Sherlock puts himself on the same level as Mary; later he even has his own vow to make. And John himself had prompted this view, when asking Sherlock to be his best man. In the speech Sherlock is proclaiming his love for John, and the ending of the episode make it even more painful, because Sherlock is left alone, looking sad when John can’t see him. And so he leaves. Who leaves a wedding early? Maybe someone who is in love with someone he can’t have. Sherlock did his best to give John a great wedding, he had put himself out of his comfort zone, and Mycroft knew exactly what was going on when he said: don’t get involved. Sherlock is not just involved, he’s in love. With someone who’s just got married to someone else.
So, when we find Sherlock again in HLV we know that he’s started doing drugs again. He says that it’s for a case, but can we be sure that it’s only for the case? When they’re back at Baker Street John notices that his chair is no longer there. Given how wistfully Sherlock was looking at it in the previous episode we can infer that having it around was too painful, so Sherlock moved it out of the way. (Incidentally, the chair comes back when Sherlock knows that John will most likely go back to Baker Street because…well, because Mary is not who she said to be.) Similarly, drugs could have been a way to escape loneliness and pain. We all know that Sherlock doesn’t die only because he would be leaving John in danger. I think this speaks for itself. If it’s not love, I don’t know what it is. In the rest of the episode Sherlock goes out of his way to help John, saying that Mary didn’t mean to kill him (which is up for debate, and personally I think he’s lying), trying to reconcile them (while wounded, and enduring John’s harsh remarks) and finally, shooting Magnussen because he was a threat to John. As a consequence of shooting Magnussen Sherlock is sent on a mission that is most likely going to end in his own death. Still, while saying goodbye to John for what should be the last time Sherlock tries to diffuse the tension and make John smile. Then, when he’s alone on the plane, Sherlock looks broken. This episode really hammered us in the head with Sherlock looking sad when John can’t see him.
So, I’m personally convinced, as many other fans, that s3 has been about Sherlock’s realization that he’s in love with John. He has been for a while, but s3 has been his epiphany. And a rather painful one, given that Sherlock himself has made the mistakes Irene had done. He let his heart rule his head. For John. And we are not sure everything is going to turn out for the best.
Finally, there are a couple of other things that might support this view. In TEH Sherlock used an expression (he helped a guy put up some shelves) that by some has been interpreted as a reference to sex. I didn’t know what it meant, but it is definitely interesting, especially if connected with his lack of interest for women. I’m not forgetting the little bit about his preference for “normal porn” that we got in HLV. Personally, I think normal was to be interpreted as “not kinky” and not as “straight”. But maybe that’s just me. Furthermore, Sherlock said some interesting things about being “different”, both in TEH and in HLV. I have already written about this here, so I’m not going to discuss it further. (The idea of Sherlock Holmes being gay is not new, and I wrote something about how it’s a thesis supported by scholars here.)
Conclusion: as of s3, Sherlock has realized that he’s in love with John. And where do we go from here?