I'd agree that the Flood's introduction in 343 Guilty Spark is very creepy and uneasy, particularly if that was your first time learning about the Flood. What's even scarier, though, is playing in those tight corridors immediately after the Flood's arrival in that mission. Playing in such small areas in that section is really nerve-racking for me, as the Flood jump around corners and leap towards you, as you try to shoot them down as quickly as possible. I'd get freaked out by that part, and it was quite terrifying, to be honest. Plus, there's some really good storytelling in that mission, as you notice the piles of dead Marines had disappeared; they became the Flood you were then fighting. It's a small detail, but one that makes the mission just that much eerier. So yeah, the entire 343 Guilty Spark mission is probably the scariest part of the Halo franchise.