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The entire opening song surprisingly fits this as well. It's a very somber, slow-moving piece that primarily features Bond surrounded by death, setting the tone of the film. Gets worse when you realise the song is from M's perspective.
Sévérine's execution. Gets even worse as Bond seems to either be taking The Stoic to its extremes or just not giving a shit (though his violent takedown of Silva and his men moments later indicates that it was the former).
Sévérine's situation in general, particularly her reaction to Bond telling her that he will do his best to kill Silva. Her laugh and the look on her face just show how desperate she is to be free of the guy.
For car enthusiasts or old Bond fans, the destruction of Bond's classic Aston Martin DB5. Gets worse when it cuts to his face when he realizes this. James Bond, the man who's been mostly desensitized to death, shows genuine anger for his car.
For someone who has either seen the film before, or knows that M is going to die in the end, the third act can be overwhlemingly emotional, as Bond prepares for battle in the place of his birth, using only the bare essentials. It is a very ominous scene, knowing that the storm will strike, and that it will do horrible damage when it does.
As it turned out, Silva still loved M enough as mother to want to "make peace" with her (according to his twisted logic) by sharing a painless-death together. When realized she was painfully and mortally wounded by a stray bullet from his thugs, all pretences of arrogane and wit crumbled into a tearful little boy, lovingly embracing his mother and begging for her forgiveness. It was actually quite a pathetic yet oddly endearing moment of humanity for a villain who had been nothing but monstrous up to this point.
Even worse, M is dying in the small chapel connected to Bond's childhood home, the same place he most likely had to cope with the deaths of his parents.
Look at Bond's face just after M dies. He looks like he honestly has no idea what to do. He just looks...lost.
This woman, via Judi Dench's performance, was the epitome of the Iron Lady. But alas, she too is human, and very much die.
"When I told him his parents had died, he hid in here for two days. And when he came out, he wasn't a boy anymore."
The opening scene. M orders Bond to leave his compatriot agent to bleed to death. The look at the agent's face is utterly heartbreaking.
Silva's backstory. One of the few moments when you genuine feel bad for a Bond villain in contrast to the precedessors who were simply evil and irredeemable.
The scene in which Silva demonstrates the horrible effects of the failed suicide pill. You almost want to let the guy off the hook for his mad spree.
For this troper, the scenes of Bond struggling to reacquire his atrophied skills was strangely tearjerking. Perhaps it was watching a man who was the pinnacle of stoic snark and suave cool, now reduced to fumbling about, futilely trying to use skills that have clearly eroded. It was a pointed example of the film's overall theme of decay.