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In the last scenes of Skyfall when Silva finds M in the chapel, he looks around and speaks

Of course! it had to be here. It had to be this way.

What was he talking about? Was he referring to something that only he and M knew?

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It's not about something that only he and M knew , it's about the place and the situation that they were in.

Silva hated the whole institution of MI6 of which M was the Head. His hatred for M was much more as M was a mother-like figure to him. Later he was sacrificed by his organisation for the exchange of six prisoners in China and he held M to be responsible for that.

To Silva, that(mother abandoning her child) was a sin. M giving order to the agents to kill people are also sins.

.....and sending her a message advising her to "think on her sins" before bombing her office ...

Source

So, when they meet each other for one final time, Silva sees it is in a chapel. He knows that, he (the child) has and still is going to commit a sin(killing M) and M has also done many. He thinks it couldn't be better than a chapel where the one who had committed sins will get justice and mercy both. Hence he says,

Of course! it had to be here. It had to be this way.

  • Thank you for the answer! – naive Mar 19 at 14:53

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