So the ending went like this...
Batman used the Bat to take the nuclear bomb out to sea to let it explode there so he could save Gotham City. Which would make people think he died but in reality he didn't because that one scientist told Lucious Fox that Bruce Wayne fixed the Bat himself 6 months ago so that's how the Auto-Pilot thing worked. Then we see James Gordon looking surprised because while the city was now hailing Batman as a hero by building him a statue, there was no purpose to owning a bat signal if there is no Batman to come. By leaving John Blake the coordinates to the Batcave and restoring the bat-signal, he was gesturing to Gordon that if ever the city needs Batman, he'll be there. It's obvious that he's looking around for Batman after finding it restored. We also see before hand ...Alfred, James Gordon, Fox & Blake at his burial an Alfred starts crying and saying that he failed bruce's parents in which in he didn't which he later found out.
Later on we see they left something for Alfred when they're dividing up Bruce Wayne's assets, they note that Martha Wayne's pearl necklace is missing. If you recall, there's a tracking device on it. I've read that it's implied that Alfred followed the transmission, leading him to that cafe in Italy. Only then he notices Bruce along with Selina Kyle at a table an gives him the head nod as if the image he had in his head from earlier in the movie were true because bruce came thru in the end an saved everything himself. Though to the public eye bruce was dead and so was batman until Gotham needed him again. Funny thing is most people forgot the device he gave to her to wipe her identity and crime records from the system entirely so nobody would know about her anymore.
Finally in the end we see Blake in the bat cave trying to figure that place out only then he steps on the platform which indicates... "The Dark Knight Rises".
If people ask you why or how can James Blake become batman himself without training ...the answer is simple an it came from when Ra's Al Ghul said this to Bruce in the Batman Begins movie....""The training is nothing, the will is everything. The will to act."
