So the scene where Sherlock goes to identify Irene's body at the morgue. Please bear with me since I am not sure if this has been already talked about and probably ages ago.
Sherlock had assumed that they are going to find Irene dead because she sent him her most prized possession - the camera phone.
He takes a look at her face - we are told it is bashed beyond recognition. He asks for a look at her naked body, all of it.
Now, we know Sherlock was a bit perplexed at Irene's (a woman's) naked body being shoved in his face.
But he is still Sherlock and he did have the time to deduce her appearance up until the time John walked back in the room and then he decided to offer his coat to her.
Back to the morgue - Sherlock sees the dead woman's naked body for a few seconds, rolls his eyes around, and says "That's her" with confidence.
He wouldn't have concluded it's her if he wasn't sure. If he's sure, how did he miss that it's not actually her body? He has noticed and deduced loads of bodies through his career - dead and alive. He could not have been mistaken or taken a guess in this scene.
Which means he lied. He knew it wasn't Irene's body.
Why would he lie? Because The Game is On. He understood that for some reason Irene wanted them all to believe she was dead. So he let them. Also because she needed protection. Sherlock, without all his walls and masks, is an extremely caring person. Irene hadn't committed a viable crime up until then technically. She just had information. He wanted to see what happens next.
Now, everyone - including John, Mycroft, and the audience assumes Sherlock is heartbroken and sad up until then because of Irene's "death".
But we know he knew she was alive. Why was he sad then? John says
So, it is not specific to Irene's incident then.
Sherlock witnesses that John doesn't deny.
Then the text alert goes off and Sherlock hurries off from there.
Going (walking all the way?) home like this
He is clearly shaken, in deep thoughts, a bit confused, and is trying to gather himself.
Why? Because, hey look! Irene is alive? Obviously not.
For a man of Sherlock's calibre, intelligence and standards do you really think he would get all emotional and shaken up or even fall for someone some woman who literally beat him up for her camera phone? Who used him. Who drugged him. Who said he'd make an "unattractive corpse". Who asked John to back-stab him. With who he had no emotional connection whatsoever? Please.
I mean I don't have to go on about it since it has been established that Irene is a Sherlock mirror. So many metas on this.
He was like that because John didn't deny Irene's "Look at us both", John was so jealous - angry jealous (his reaction to "Are you jealous?" was a deflecting "We are not a couple"), him accusing Irene of flirting with Sherlock - questioning her like a possessive partner, John denying he's gay again (nothing new there) but actively doing everything that proves his attraction and love towards Sherlock.
It made Sherlock panic even more knowing that what he had been feeling, rather - what he had been trying not to feel is also, maybe, felt by John too! For a man who keeps a tight lid on his oh-so-strong emotions, it must've been a really intense experience.
It's all there for us to see, we only need to observe.
