Harold reluctantly agrees to help John protect a young woman who is participating in a dangerous and deadly game, meanwhile Shaw works with a group of thieves as her new cover identity.
We seen the new Batcave at the end. There are loads of old tunnels and rooms underground like that. London Underground has just realised that it can make money by renting them or selling them off.
The idea of that kind of game used as a recruitment tool has actually been used by software developers and possibly even by the secret intelligence gathering organisations too. This one seemed a might bit complicated. I can maybe believe that one or two people might play it for a year to the very end, dropping out of college, on the run from private security companies; and that maybe one of them had no parents or strings attached of any kind. However, it is a stretch to believe Samaritan was able to find operatives this way in every city in the world - or even in the few that were mentioned (which I forget now - Tokyo was one.)
Harold didn't try very hard to turn the girl on the observation deck. He should have told her the whole story, everything. If she believed him them she could work for Northern Lights/Prism/the Machine and the secrets are kept. If she didn't: well now she is working for Samaritan anyway; she knows who Harold is and she will have been told all the rest of the story in any case. Now she is a formidable enemy rather than a formidable ally.