In the moment they'd rescued her, he'd known. He knew that the scenario he'd managed to convince himself of, where Elizabeth would be reinstated at the leader of Atlantis and left in peace, was never a realistic expectation, but he'd allowed himself to hope. Worst of all, he'd persuaded her to hope too.

So little had been said when she walked back through that gate to be immediately rushed into an isolation chamber where a series of medical examinations were performed to ensure she wasn't a threat to either Atlantis or the inhabitants of it. He knew that the discussions were ongoing with the IOA and SGC, but he had purposefully been shut out of these discussions while Elizabeth was poked and prodded at like some lab rat. Hoping to gain any semblance of information, he had cornered Sam and casually asked how discussions were going, and while she said very little, her eyes said very much and that 'very much' wasn't good news.

As a man of the military, of action, he'd been frustrated to the point of rage, finding himself snapping at both his team and his superiors as he found himself increasingly helpless. Eventually, even though Elizabeth had cleared her medical, he stopped visiting her knowing that he could only kill off a little more hope with each visit. The hope was finally killed off when Richard Woolsey quietly took him to one side and informed him of the decision reached by him and his colleagues, offering that John should be the one to tell Elizabeth himself. Although Woolsey spun it as being the kindest solution, John knew that it was cowardice really and part of him wanted to watch them squirm as they were forced to do the deed themselves. A big part knew it had to be him though.

When he told her, she didn't cry, or shout, or even show any indication of disappointment. Instead, she just nodded politely before packing her few belongings into a bag ready for the journey ahead of her. Her calmness unnerved him, and all the things he wanted to say were momentarily lost in his confusion. He'd never been a man of words, and the words he'd been rehearsing had decided to leave him when he was most depending on them. Saying nothing herself, Elizabeth had turned to him and squeezed his arm gently before turn her back on him and walking away to the fate that waited.