Ok, but what if
Jon is NOT gone.
I described in length here why I don't think Jon reintegrated into Sherlock's psyche at the end of Chapter One and how I think he is just gone.
However, there is an additional theory I have and I would like to talk about. So what if Jon is gone but not GONE gone?
This rambling is based on overthinking every line in these games, so keep that in mind as you continue reading. Also, I'm likely coping very hard here because I love Jon with all my heart.
First and foremost, I will treat Jon as a sentient being here. I imagine Sherlock and Jon like two flowers planted in one pot. Jon is a personification of Sherlock's love for life and himself; still, Jon is portrayed as having a consciousness. He not only has his own opinions and personality, he also has feelings. E.g. he describes the feeling of being ignored by Sherlock as a "punch in the gut ", he experiences anxiety when forced to face the nature of his existence, etc.
To explain why I don't think Jon vanished completely, I will start by explaining how I read the events of Chapter One from Jon's perspective.
Sherlock created Jon because he was lonely; he wanted to be happy and loved, so he placed his own self-love into Jon and made him his biggest fan and a neverending source of motivation to pursue the more fun parts of life. Jon provided a certain balance in Sherlock's life and also acted as his moral compass. However, Jon struggled with the nature of his existence from the very beginning. The memory at the theatre shows him being distraught by the audience's inability to see him. He refuses to keep this memory; even when he and Sherlock recall it ten years later, he never addresses it in his diary. He jokes about how excellent his performance was, but he is in denial that it ever happened the way it happened. The memories hurt Jon, who feels like a real person but never gets to live as one. The only thing in Jon's life that affirms that he exists at all is Sherlock, and it's a great source of anxiety to depend on someone so completely.
During Chapter One, we witness the impact Sherlock's memories have on Jon. He asks Sherlock twice to let it go because the memories hurt him, and they hurt him because he exists to love and protect Sherlock. Therefore, Jon's whole purpose is threatened if Sherlock refuses to be protected by him; in a way, if Sherlock chooses to remember and, therefore, be hurt, he rejects everything Jon stands for, everything he was created for.
And yes, I'm convinced Jon mostly cares for Sherlock's well-being, but he isn't entirely selfless either. There isn't a conscious being that can be entirely selfless. He is in the unique position in which every single action of another person is directly tied to him and affects him. Every time Sherlock chooses not to listen to him, his role in Sherlock's life becomes more and more unsteady, which terrifies him. They can't be close and united if they don't share the same values. I think the worst thing that could happen to Jon is to end up being irrelevant and ignored by Sherlock, but being forced to continue existing regardless.
Now, I will just post this journal entry, which Jon writes if Sherlock ends up killing someone.
This is how this reads to me: Jon can't bear watching Sherlock become a murderer, but he is not only concerned for Sherlock; he also doesn't want to feel the pain of watching Sherlock change like this. He doesn't want Sherlock to alienate himself from him. This is what I mean when I say that Jon is not selfless. He doesn't want Sherlock to be hurt, but he doesn't want to hurt either. Another thing I see here is him posing the question if the has a choice, and at least at this point, we can conclude that the answer is no. This is an important point for this post.
Now, I will come to the end of the game. After Sherlock enters the garden and begins regaining his memories, we have yet another scene of Jon begging Sherlock to talk to him and saying he is scared.
I think this shows pretty well how anxious he is about becoming irrelevant or even invisible to Sherlock. The end scene in the garden is everything Jon fears slowly coming true. And it doesn't end there. No, it culminates with Sherlock denying to acknowledge Jon as a person.
And this, in my opinion, is the moment Jon knew he wants to disappear. He barely interacts with Sherry after this, except for asking why Mycroft is there after Mycroft poses the question if "Jon is worth it". We still don't know what Mycroft means, but it's implied he thinks Jon isn't worth "it", which is kinda rubbing more salt into Jon's wound haha :'). Hell, Jon doesn't even intervene in the scene where Sherlock pulls a gun on his brother, he stays on the bench.
As I said in my previous post, I see all four endings as bitter. Even in the two endings in which you blame Otto, the last interaction between Sherlock and Jon lacks the usual warmth between them. I think it's because Jon is quite bitter himself. He is hurting a lot. He tries to reminisce about their times together and says his life hasn't been wholly in vain, but he is just done with it at this point. He is leaving, but not only for Sherlock's sake; he is leaving because he can't bear the pain of staying with Sherlock after being called a lie by him, especially because Sherlock hates lies. Jon has protected Sherlock for years, but Sherlock thinks it was wrong, and Jon's whole purpose is put into question. Sherlock has always been the only person to believe in Jon, and from Jon's perspective, he no longer does.
Don't get me wrong, I don't think he leaves out of spite. I simply think he'd rather vanish than feel obsolete.
I think this post is getting rather long, so I will just get to the point. Why do I think Jon is not GONE gone? Because he implied he has no choice than to witness what's happening to Sherlock, no matter how much it hurts him. And because Sherlock keeps addressing him during The Awakened in a way that suggests, that he still might be somewhere.
Yes, Sherlock misses Jon and he is desperate, so him talking to Jon shouldn't mean much in this regard, but still, Sherlock doesn't seem to believe that Jon is gone.
He seems to believe that Jon is still watching him from somewhere (from Heaven? Why are you looking at the ceiling, Sherry?) and is fully able to make an appearance and "intervene" if he wants to. Of course, Sherlock doesn't know everything, but honestly, I agree with him. Because why would Jon have the ability to erase himself from existence? If he could simply erase things, he would have likely erased Sherlock's memories of Violet's death. However, he has the ability to conceal things, like memories, so it's not unlikely that he can conceal himself too.
I think Jon is still somewhere deep inside Sherlock's mind. We already know he can disappear whenever something makes him uncomfortable (like Dilwyn), so I'd like to think that he disappeared in the same way during the ending too. I think he is dormant right now. And he is hurt. But he is there. I don't think Jon can die unless Sherlock dies.
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