After the cut-scene I was taken to a Master Chief level, where Master Chief was fighting off a literal flood of the flood and he was able to escape. But that is when a Flood Arbiter level started up the opening cut-scene with an early flood drop-pod in New Mombasa. The level started with an option to get out of the drop-pod. So when I did, the level officially started. Once when I was playing, I was able to send the flood to kill the citizens of the city. The level ended with Flood Arbiter killing Master Chief and turning him into a flood combat form. The next three to four levels were based on taking over the city. On the final level of this screwed up version of Halo 2, it showed the Earth in a dead state with no signs of life whatsoever, and the Gravemind had taken over everything on Earth. The final lines in the cut-scene were spoken by the Gravemind. They were "You have brought this on yourself Izzy". He continued. "You cannot undo what has been done. This is the way the world ends". The cut-scene stopped on that note. After that I searched through the game files for any bit of coding dealing with that cut-scene, but there wasn't anything. All I found was just files for unused character models and vehicles.
Another such event was in Halo 3, where there is a glitch where you can cause a "half flood" character spawn. This has happened to me on several occasions. When I was playing Halo 3, it was first released. I found out how to perform the half flood glitch. It was very fun to have flood allies before you were supposed to. I did this glitch a lot and I eventually saw writing on their backs. The writing lead to finding an aster egg Bungie had put into the game. When you do what the messages told you to, you will eventually get to doing the glitch on an Elite. But once you do, the elite will kill you. But you will come back to life as a half flood Master Chief and you'll get a special suit of spartan armor for multiplayer. It is covered in skulls.
Another thing is I have just been generally afraid of the flood since Halo:CE because they are so creepy looking like the flood tank form and I have had many nightmares due to the flood from the Halo series. This next paragraph will be about it. I was in High Charity from Halo 2 when it was being over run by the flood and I was trying to fight them off using a shotgun and the magnum. I was accompanied by Master Chief and The Arbiter while I was fighting them off but almost every flood infection form evolution came, even the unused flood juggernaut. We were easily defeated and I was killed by the flood tank form by being impaled by its mutated right arm. I immediately woke up after being killed and after that I couldn't stand playing the Halo 2 campaign after that nightmare.