It isn't the Flood :P
Kidding aside, I can kinda see it but I would really rather it not be tbh. The focus of Infinite seems to be the banished, I feel like bringing the Flood back again would kinda take away from that as they would ultimately have to be the main focus again.
That depends on how they are introduced and dealt with. If they make an appearance, they could be in a pre-proto-gravemind state. And with the Banished already proving to be seasoned in dealing with Flood outbreaks, they along with Halo's own defenses and whatever efforts you make against it could contain the outbreak before it becomes more than a minor bump in the story.
Even in CE I struggle to think of the Flood as the "main villain" of the game, like they more clearly were in 2 and 3, since the outbreak was contained to Alpha Halo and posed minimal immediate threat to the galaxy as a whole. Guilty Spark instead was the ultimate antagonist of that game, your primary goal towards the end was to stop him from firing Halo, not to stop the Flood, you just killed two birds with one stone.
Also the sounds could be Crawlers, if the Promethean make an appearance. They do make similar screeching and jittering sounds to the Flood at times.