[He can't do anything. He's so frustrated. There's so much at stake for everyone involved, and the only way forward hurts his brother. ...Maybe....the reason he can't protect him is that Shirou was always the defender.

"Not without probably sacrificing the only friends he has." Because while Atsuya would protect Shirou, he couldn't protect the whole team. He doesn't want Shirou to be alone again. Look what that did to him. Getting rid of Hitomiko...would probably let the aliens slaughter everyone.]