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There's also the moment where James inherits her Union Jack bulldog, which Bond hates, in accordance to her will. Bond interprets this gesture, more or less, as "don't have a desk to put this on".
The final scene with Bond, Moneypenny, Tanner and Mallory (now as M) in the new (or rather, old) MI6 office brilliantly reminds us that no matter what happens, however much things change, James Bond WILL return.
Combined with From a Certain Point of View. After Bond returns, M tells him he will have to take several tests again to return to active service. According to M, Bond passes the tests. Silva reveals later that Bond in fact failed the MI6 active service tests in an effort to convince Bond of M's history of lying. What M never said was what tests he passed. In M's eyes, Bond has "passed" tests of character that would go above and beyond official results.
Or, in Bond's eyes, M is willing to stick her neck out by letting him get back into the field.
Although he loves to snark Eve over accidentally shooting him, it's clear Bond doesn't hold a grudge over it.
Bond orders Kincade to leave, in order to prevent him from suffering a Mentor Occupational Hazard. Kincade bluntly refuses the offer, addressing one of Britain's most skilled professional killers as a "jumped up little shit." Bond needs to protect M, and Kincade will not let the boy he cared for do it alone.
When the assault is in progress and the Skyfall lodge explodes, Kicaid and M look back with extremely worried looks.