Does anyone else think about his final word to Harold in Return 0?
The way he said "me and the machine have had a long standing agreement-a deal- told you. Pay you back all at once. It's the way I like it"
When did he make this deal? When he had God Mode in God mode(2.22)? During Contingency somehow? Has he spent the last 3 or so years content that he'd either dying rescuing people or saving Harold? What if he made this deal after they lost Shaw? Or when they had an open system in the beginning of season 5? He knew since early on he'd die for Harold but when did he codify it!?
Also pay him back all at once! So John truly believed he couldn't pay back the incredible favor Harold did by using John to assuage himself of his guilt from 'letting' Nathan die by dying for him!
The fact that he said this: "This is what I do remember when you came to me you gave me a job, a purpose, at first I'd been trying to save the world for so long, saving one at a time, seemed sort of anti-climactic."
Because yeah- saving one person seems small but over time you truly see the good their doing. number come back to help them (Zoe, Elias, Carter, definitely ... but also Harper, Joey, and Pierce- Even Control in her own way that team machine will likely never know know about.) You see what happened when John stopped swooping in to save the day during Pretenders and what it means that the machine was made by someone who truly thought about the implications of what he was building (and he'll be the first to admit it's not perfect!) But we literally get to watch the show build up into an action-packed and climactic series finale (pretty much the entire season 5 is so high stakes it's really impressive)
and then he finished off with "But sometimes one life if its the right life- is enough. Goodbye Harold."
and then you have to watch Harold being just as helpless as you watch John die (I don't believe he's dead but that's the experience of watching it so.) And he deliberately choose his last word to be thanking Harold and prove to him that they did THIS right. That he needs to be the one who lives- and affirming Root's sacrifice as he does so too.
It's also reminiscent of his opening words in the show, "When you find that one person who connects you to the world, you become someone different, someone better. But when that person is taken from you, what do you become then?" And he knows that Harold is one of those people for so many (including him). The world as a whole cannot lose him because he makes i better.