"Multiple protagonist" is something of a misnomer, and I can't think of a game here that was successful using multiple POV (which is what this is) vice having a protagonist and tell the story through him/her.
Multiple POV works fine where the author wants to keep the audience emotionally at least one step removed from the story. GRRM and JRRT do this well, but it takes many books to pull it off. For games, that's not a luxury and author can afford. Better to decide who the protagonist is and tell the story from that character's POV. Multiple-POV may make things easier in the short term (because the author doesn't have to explain how the protagonist comes across some specific knowledge), but it's much less interesting to write and far, far less interesting to play.
I'd advise the author here to pick a protagonist now, while still early in the story, then figure out how to convey knowledge to the protagonist and hence to the player.