John nods and he's listening to everything Finch is telling him, though he's quiet for a moment as he considers everything this might mean. There may not be a Machine in Darrow, there may not be any way -- currently, anyhow -- to create a list of numbers, but what they're talking about is still going back into a dangerous life. It isn't for himself he hesitates, but for Finch.

He won't ever have a normal life and he knows it, but Finch still has that chance. It's doubtful he'll take it, not without Grace here in Darrow, too, but John has to at least give him the option. It has to be said aloud.

"This is what you want to do." It's a statement more than a question. "My commitment to any plan you make is complete, Harold, you know that, but I think we should be sure this is really the path you want to take again." He has a chance here for something else. John doesn't say that part, leaves it unspoken, but he thinks they both know what he isn't saying.