Good question. My guess is Issac paid for an implant otherwise Visceral done goofed. If the writers were smart they'd address this during the initial scene before the crash and separation. It literally would only take seconds and one line of conversation.

Now if the whole Red Marker being a huge dick and manipulating Issac through hallucinations of his dead girlfriend plot twist of the second game didn't happen? Then yeah... I'd be all for Ellie being a vivid figment of his imagination.

...

Or they could go the ultra generic route and brainwash her into a Unitologist agent. Right now I'm much more interested in what they have done with Carver's Marker dementia. Really hoping the guy isn't just scenery with a gun and a mouth here because I wouldn't be surprised if that meathead replaces Issac as lead in the next game.

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