In the ending of Skyfall, Raoul Silva dies at the chapel, M dies of her wounds, and MI6 is rebuilt around Gareth Mallory as the new M, Eve at a desk and a Bond ready to work.
To break the finale into steps: Bond takes M to Skyfall, his childhood home in Scotland, and they set traps with Kincade. Silva's men attack, the house is destroyed, and M is badly wounded. Silva follows them to a nearby chapel, where Bond kills him with a thrown knife. M then dies in Bond's arms.
Why does it matter? Silva's aim all along was to kill M, and his attack left her fatally wounded even though he died at the chapel. The villain's plan, in other words, partly succeeds. It also answers the film's opening. In Istanbul, M orders Eve to take a shot she cannot make cleanly, and Bond falls into the river. The decision to sacrifice an agent is the same kind of decision Silva blames her for, since he says she abandoned him. The story closes the loop by putting M's life in Bond's hands at Skyfall, where he cannot save her.
The aftermath shows where the series goes next. After M's funeral, Eve says she is leaving fieldwork for a desk job as secretary to Mallory. Mallory takes over as the new M, and Bond says he is ready to get back to work, which sets up a more traditional Bond team going forward. That is a change from the previous entry, Quantum of Solace, and it is the setup Sam Mendes inherited when his return for Spectre, again with John Logan writing, was confirmed in July 2013.
The film also came out in the year marking 50 years since Dr. No in 1962, and Mallory's takeover, Eve's desk and Bond's return to work read as a reset for the franchise's next stretch.
My opinion: the destroyed house suits a 50th anniversary film, because it lets the series burn the past and keep the habits it likes. There is no post credit scene, so the ending is the final word.