THOUGHTS
In many ways the city empathized with Doctor Weir. Atlantis had spent many years alone with only the tenuous thoughts of her distant sister as faint company. Though the doctor had not spent as many years alone in this command as the city had been alone, the comparison was apt. Atlantis knew the feeling of having no control, of being at the whims of others, and it was not overly pleasant.
At the same time, Atlantis felt she had no choice. She wanted her sister back with her, and now there were people who could not only deliver her, but who could and would defend them both until their last breaths to keep them together.
At the end of the Ancients' battle with the Wraith, even her guardian, protector, and bonded friend had had little time for her. Without communication, she had no eyes, no ears, and no voice. By the time the Ancients left to return to Earth, her old home, her conscious mind had all but been forgotten. They had promised to return, but when her children had not returned after ten years, she had known that no one was going to come back. She had been forgotten.
Had anyone thought to ask her, she would have chosen to be destroyed rather than sit waiting for a return that might not happen.
So yes, she understood what Elizabeth was feeling, if perhaps the humans emotions were on a smaller scale than her own. It was because of this that the ancient city decided to do something she rarely ever did for people who were not part of her intimate circle of protectors, friends, and doctors; in fact what she was about to do she had not done since nearly fifty years before the Wraith ever besieged the Ancients in this galaxy.
She was going to speak to one who did not normally open their ears to her. She was going to explain everything to Elizabeth Weir.