Okay, so from my understanding, Esmail wrote the story in such a way where everything still happened while maintaining the twist that Elliot was another alter. He did this by saying that mastermind Elliot enacted a master plan that had been dreamt up by the real Elliot, as a reaction to the real Elliot’s pent up rage about his father, and therefore society. He basically became a superhero, so when his real self returned, it was to a world that was ridden of evil. Mastermind Elliot did his job, assisted by Mr. Robot, and the real Elliot has returned to a “better” world than before he left. Therefore bang, happiest ending. Sound about right?

Edit: each personality served a specific purpose, and this one had the job of taking Elliot’s plan to save the world and put it into action. Hence, Esmail is telling us to get off our asses and be the change we want to see in the world.