I imagine by the end of the game, we’ll see how the Flood got aboard the Spirit of Fire, due to us seeing that Infection form scurrying through the cryobay. If I had to guess, they’ll land on some Forerunner facility world and accidentally encoutner the Flood while fighting this other party with that Jiralhanae. If you had to guess, will we see how the Flood got aboard the Spirit of Fire and if the crew survives?
Or they already explained how? Infected crew, they tried to sanitize the ship before they left the shield world, but they didn’t get it all.