Mary shot Sherlock for the same reason that John shot the cabbie in A Study in Pink and Sherlock shot Magnussen at the end of His Last Vow: sentiment.
John is Mary’s pressure point. There is nothing she would not do to protect him. Even if it means killing his best friend. It’s not understandable for us as an audience because we see this from Sherlock’s point of view. He is our main character. And Mary shot him.
But what if Sherlock would have shot Mary for the exact same reasons as she shot him, wouldn’t that have been plausible for us? That Sherlock would do whatever it takes to protect John? Because that is what Mary is doing in her own way, perhaps it’s not the right way but she’s doing it because she loves John, nothing else.
“Love is a much more vicious motivatior”... I couldn’t find a plausible explanation why Mary would shoot Sherlock but now I have and this is it. Love.
No, a thousand times over. She shot him because she is selfish and would rather keep John to herself and see him mourn his best friend (a process which almost destroyed him and which she witnessed firsthand) than buy herself time by knocking Sherlock out instead of shooting him, or negotiating with Sherlock to keep her secret. This isn’t love, it is greed and manipulation.
What hazeltea said. Mary’s action was out of a very selfish love. She chose to risk the death of John’s best friend—the man whose loss nearly BROKE HIM the first time—rather than TAKE THE RISK of losing John’s affections (as we see later, in fact John does accept her).
Contrast this against Sherlock’s love for John which, even when they are at their worst with each other, includes Sherlock being willing to put his life on the line and also handing John off to the love of another person even though it means he will have less of John’s time and attention for himself. THAT is selfless. (Not that Sherlock is always selfless when it comes to John, but he’s got a hell of a lot better grasp on it than Mary does.)
Mary might have called an ambulance for Sherlock, she might have given him a chance, but it was ONLY a chance. She did NOT save his life, no matter what Sherlock argues to John. For one thing, she’s the person who made the ambulance necessary in the first place. If you stab somebody and then sew it up for them, it doesn’t negate the stabbing.
For another, WHERE she shot Sherlock. In the upper abdomen, just below his rib cage. Do you know what’s there? Stomach, liver, intestines, spleen.
That is all soft tissue. Very delicate tissue. A gunshot wound acts on the soft tissues of the human body like an impact in water or a sonic boom in the air. It creates a traumatic shockwave that ripples out from the bullet hole itself and through the tissues to rupture and crush them. In fact, for a split second after the bullet enters the body, it creates what’s called cavitation. This basically means ‘the splash.’ Living flesh is actually smashed open in an entry channel significantly larger than the bullet itself (this is why higher caliber is so much more damaging; the cavitation is significantly greater) and then pushes closed again. All those soft, delicate, easily damaged organs in there—any or all of them could have been damaged beyond repair.
Granted that the suppressor would have slowed the bullet and removed some portion of the force that does the worst of that damage. But even if she was such a perfect shot she could thread the bullet between the stomach, intestines and spleen, all that would mean is that it had a chance of damaging all three.
Mary’s ‘surgical shot’ was more accurately a great way to doom someone to a slow, especially painful, almost certain death. The only reason Sherlock woke up again was because she was LUCKY, and Sherlock was too stubborn to die.
Or because the writers have decided to go for the Hollywood approach to guns.
This is not to say you should hate Mary or assume she doesn’t care about John. But understand that she is, as CAM said, very much not a good person. People who can kill others professionally are seldom angels aside from that.