They are together once again, the two of them. He is with his new toy, she doesn’t like this one, this one is too demanding of her Doctor. But sooner or later she will be gone and it’ll just be her and hers again. She makes sure the girl knows this. She is not about to be replaced by any stray the Doctor brings home to her. Because at the end of the day, at the end of the year, at the end of all of time, the Doctor is hers and will return for her like they will for none of their companions.

She likes some of them, River Song makes him happy, but River Song is but a chapter in their adventures together and the TARDIS knows that the first iteration of her doctor would have disliked the headstrong River Song. Each iteration brought home different friends but each time they brought them home, to her. The girl is right, the TARDIS is jealous sometimes of his various lovers, but once they get to see her, in a weak, human vessel but the girl is in front of him and he only has eyes for her deteriorating body.

Yes. She may have chosen The Doctor but the Doctor had also chosen her, and continued to choose her every time he came home willingly, with a pet in tow or fresh from leaving one behind. They changed but she existed outside of time and space, they belonged together like no other in the universe, the TARDIS and her Doctor.