A whole new meaning

Mr.Robot kept shooting Elliot in the head to get him ready for Season 2's finale where he gets shot by Tyrell. He knew Elliot would probably fuck up the plan by trying to be the hero and he did what he felt he had to do by getting Elliot shot with the slim hope that he doesn't meet a fate worse than death from the Dark Army. When Elliot didn't think the gun was real, there was less of a chance for the third personality (his agressive tendancies) to override him and lead him down an even more self destructive path.

Throughout the show, Mr.Robot has tried to mentor Elliot andead him down more positive prospects by either alienating him from things like Fsociety or trying to be a protective father who takes beatings and abuse for his son. He takes the fall out of the window in season 1 by making Elliot think he's a real person and he only ever hurts Elliot to keep him from getting in a worse situation. His insistence on working with the Dark Army was too complete their plan and when that failed his focus was on keeping Elliot alive, hence why the roles seem to have reversed. The thing is, we're seeing Elliot from a third person perspective now and without his narration, a lot of his actions seem outright evil or like they're crossing a line. Truth is, he'd already crossed that line in Season 1, as more of the plot is revealed, the parallels and foreshadowing smacks us in the face even harder.

Mr.Robot is the father Edward never was, and the show has gone out of its way to display it. If Edward and Mr.Robot were the same person, he'd have let Elliot commit self destructive actions and hurt innocent people because he was his 'friend'. Mr.Robot gives Elliot tough love because he's his 'father' in every sense of the word.

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