These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Dakota panicking on her first day and not understanding why being shot and killed is a regular part of the team's existence.
The reveal that Team Phoenix is made up of humans in people jars, with a plug installed into their right eye horizontally.
After they leave the game world, Team Phoenix becomes deathly ill due to clone degeneration.
The ending of the book. It's like the "Zion is part of the Matrix" theory.
The Untwist: It's pretty easy to guess what's going on with Team Phoenix, especially if you're aware of other media that uses the twist. This is even lampshaded in the story, with everyone else guessing at it and Phoenix being in deep denial.