"But at the time I overlooked one problem of great importance; and it is astonishing to me, except on the principle of Columbus and his egg, how I could have overlooked it and its solution. This problem is the tendency in organic beings descended from the same stock to diverge in character as they become modified. That they have diverged greatly is obvious from the manner in which species of all kinds can be classed under genera, genera under families, families under sub-orders and so forth; and I can remember the very spot in the road, whilst in my carriage, when to my joy the solution occurred to me; and this was long after I had come to Down. The solution, as I believe, is that the modified offspring of all dominant and increasing forms tend to become adapted to many and highly diversified places in the economy of nature" Charles Darwin, Autobiography
I'm having trouble figuring out exactly what was missing. He knew of the struggle for existence (not all that are born make it to reproduce), he know that organisms change through time (organisms evolve), and he knew that species split through time (and those species split and so on). I suppose what is missing the 'why' - and that answer is adaptation.