Original Nathan isn't killed like they said he was at the end of season 3, but they use him to test a mind upload machine that doesn't burn off the head. However, they keep uploading and downloading him a ton of times, which begins to degrade his mind. He eventually dies because his brain is all fucked up. However, while the badguys were experimenting on him, he did convince one of them to save his memories of Nora on a ring drive, which original Nathan gives to Nora. Last scene in the series is Nora realizing the ring has Nathan's scan on it.
The AI guy they uploaded into a human body and accidentally lost in New York in season 3 ends up being their counter to the evil AI. Because he developed so much in the real world he basically achieved The Singularity himself, so they upload him back into Lakeview and he is able to deconstruct the evil AI and free all the AI it absorbed. At the end the AI guys run Lakeview as a non-profit, with the good singularity AI guy running it and the other AI helping.
Copy Nathan uploads into a body and is married to Ingrid and they are successful, so they get the happiest ending. Luke dies trying to stop the evil AI. Aleesha becomes a full-time spy for the corporate equivalent of the CIA. Cigarette Smoking Man's hard drive gets run over by a car lol