He doesn't spot her until he's almost about to leave, and by then Nathan is anxious, afraid that something really has happened to her after all, that Caffrey was right and if he displeased It, acted against the ship the way he proposed to, then it would take Claire.

He's relieved to see her. It's like a wash of nerves suddenly subsides at once, and he steps urgently toward her side, seizing her into an instant hug full of all the relief he feels in the world. He'd sent a message, but he hadn't been sure it got through--a message to say goodbye. Now he didn't care if it had or hadn't. He was alive, so was his daughter, and the ship had tried its best and failed. It couldn't break him, not that easily. It had made a valiant effort, but he'd come out victorious, and he felt more alive than he had in almost two years.

"Claire, thank God."