She was making this more difficult than it had to be. If only she’d hand Lily over, then everything could be easier. He could see that she wouldn’t let it go, that she’d continue to fight against this and while he was proud of her, he feared for her.
The Doctor’s eyes met hers and he tried to tell her that he did love her in his gaze, that she would be okay and that they’d all be back on the TARDIS soon. She wouldn’t be able to see all of that though and he knew it.
"It’s for this." Hating what he was doing, the Doctor took hold of her arm, pushed the syringe into her skin and pressed down. "I’m so sorry Clara," he said, eyes trained on hers. If all went well, she would understand soon enough, at least he hoped so.
Lily wailed as she noticed something change about her mother and he took her away from her. She pushed on him, not wanting to go with him. Standing, he faced the creature. “It’s been done. At least give us the decency to take her back where she came from.” The creature looked at him and seemed to agree. Clara was placed onto a wheeling bed and the Doctor walked alongside her. Now all he had to do was get her to her clothes.
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Lily glared at him with those eyes that reminded him so much of her mothers. She wouldn’t talk to him, even though he knew that she could speak to him through her mind. Clara was nearby and they were bringing him her clothes as per his request.
"Lily, it’ll be okay. I promise." She turned her nose up at him. So little, already so smart. Lily wouldn’t forgive him and he had less hope that Clara would too.
The other syringe was already in his pocket, waiting to be used to revive Clara. As soon as he’d been given her clothes, he’d had to act fast. Before they could realize what he was doing, the Doctor found the TARDIS key in one of her pockets, he held onto Lily, slipped the key in to Clara’s hands and held onto her.
They were gone before the creatures could do anything. He was quick as he took out the other syringe. Lily looked at him with those horrified eyes, she’d barely registered that they were in the TARDIS now. ‘Leave her alone! Don’t hurt her!’ The girl spoke in his mind and he felt relief, glad that she hadn’t lost that ability. He stuck the syringe in Clara’s arm, ignoring Lily’s protests and waited. Holding Lily in his arms, they both watched Clara as he took the drained syringe out of her arm. Now it was up to Clara, she had to wake up.