Yeah, I'm uneasy about the whole "the game affects the show" thing, because I have zero interest in the game. Crossovers are fine, but part of making a good crossover is making sure that each individual component of it is able to stand on its own without depending on the other, so that audiences who are only interested in one component aren't missing out on anything or confused by anything.
And I'm continually puzzled by the notion of how a computer game can have a canon. Every player puts a different character at the center of the action and they all experience the action in different ways -- go through the missions in different orders, have different outcomes to those missions, etc. Which of those endlessly differing versions is the "real" one where the more conventional tales like TV episodes or novels are concerned? I could understand it if the game were, like, based on
the "actual" events that happen in the show's universe -- an interactive simulation that could let people experience approximations of historical events, like the way we have WWII-based shooter games in real life. But the idea of the show responding to events in the game is more puzzling.