Yes, the Doctor had been Jack. He'd been Jack, and he'd seen how utterly terrifying it was to die. Not to regenerate, not to straddle the lines of death and life. But to die, completely and utterly.

How could Jack say that was 'all' it was? How could he think the Doctor would just easily kill him? Death was horrifying. And the Doctor wanted to protect him from it, wasn't that obvious?

He followed Jack's lead back to the surface of the water.

"Whatever it is down there, it's changing the climate of this area," he said. "And no matter what it can do, we can't let it alter your history. Because while nobody loves altering a fixed event like I do, we both know what'll happen to the universe if it does."