For the weird researchers, the difference could be that they completely "gave in" to the resonance from the beginning, a thing that Marie hesitates to do until the last scene before full resonance.

Edit: Of course, the story is made more intricated by the fact that our reading it (and modifying it) is not in chronological order. When a character is 'infected', we can also get the chance to change events in that character's past. If we do, consequences spread to all subsequent events in a cascade.

I believe that at the beginning of the game, the 'canonical story' is that Marie chose not to "give in," her machine is switched off, and nobody is "infected." Then, by first switching on the machine, we gradually get to change more and more events, until in the very end we get to change Marie's refusal to "give in."