I know, I know. There are like...three threads about the Flood already. Yes, I know. However, those threads, from what I've read, really don't talk much about how to successfully implement the Flood as a faction, they merely suggest why they should or should not be in the game, so here's my take on it all.
The Flood should most definately NOT be in singleplayer. I just can't see that fitting with the timeline. I seriously doubt the Covenant knew about the Flood prior to finding Installation 04. Cortana describes them as "scared" when they find the Flood, and says something along the lines of "they should have known, there should have been signs." To me, this says that the Flood caught the Covenant off-guard. Also, in the Halo Graphic Novel, when the Grunt calls for help on the speaker, he doesn't say "ZOMG ITS THE FLOOD!", he says "ZOMG THEY HAVE HUMAN WEAPONS, BUT THEY AREN"T HUMAN!" The Grunt is confused by these strange creatures with human weapons. And then, later, when Rtas encounters the infected animals, he seems surprised by them. He catches on quick, but that's just because he's an upper-ranking Elite officer, and they don't get to that rank without knowing their stuff.
Thus, if I am writing about implementing the Flood as a playable faction in the game, and I am not talking about singleplayer, I must be talking about multiplayer, right? Yes, I am.
The Flood would be an interesting faction indeed. Whereas UNSC and Covenant forces might start with some sort of tech yard or other central building, the Flood would start with a Photo-Gravemind (Brain Form). This Photo-Gravemind would tain the ground around it with Flood spore (an effect similar to the Creep in StarCraft that the Zerg live on). On this Flood spore, pods would grow, incubate, and then hatch into trios of Infection Forms without the player doing anything.
Infection Forms will be able to infect any infantry (dead or alive, moving or not moving), slow vehicles (like tanks), and fast vehicles that aren't moving. Infected infantry, depending on race, would either become a Combat Form or Carrier Form. At any time, a Combat Form may be turned into a Carrier Form. Vehicles, with the exception of Ghosts driven by Grunts, would remain virtually unchanged, except that they would be operated by Combat Forms instead of their original operators. Because Grunts are not large enough to sustain Combat Forms and thus become Carrier Forms, Ghosts driven by Grunts would become inactive, and could possibly be used by Combat Forms.
Flood spore would only produce so many Infection Forms per minute. It would be enough to get things going, but not enough in the later game. Thus, Carrier Forms would be vital to keep the cycle going.
Now, as the game progresses, the player will want to advance the Photo-Gravemind into a Gravemind, and then into a Super Gravemind. This is done in two ways. The first is automatic. The central intelligence, whatever it is, will pull Calcium from the ground at a very slow rate, and, if left to its own devices for long enough, evolve on its own. To speed up the process, adding Flood forms to a Gravemind would allow it to grow at a proportional rate.
Photo-Graveminds are imobile. Graveminds are slightly mobile, can produce Stalker Forms (the base for Pure Forms) once each minute, and have a special ability called Dominate Will. Super Graveminds have tentacles which can be used for self defense (making it harder for lower techtree units to kill the central intelligence), are slightly more mobile than Graveminds, produce Stalker Forms quicker, and recharge Dominate Will faster. And, of course, as the central intelligence grows, the radius of the Flood spore around it also grows, meaning the output of Infection Forms grows.
By merging a group of five Carrier Forms and a Pure Form, a Juggernaut Form can be made. Stalker Juggernauts are fast, Tank Juggernauts (these will take the form of the Juggernaut cut from Halo 2) are strong, and Turret Juggernauts have ranged attacks. Juggernauts would be the Flood's most powerful weapon.
Now, the process for achieving a Gravemind should take a little longer than it would take to get aerial units. The reason being that Pure Forms and Juggernauts are the only effective counter to aerial units.
Dominate Will is the only special (kinda like MAC bombardment) for the Flood. When used on nonFlood enemies, it causes them to freeze in place (air units sink to the ground before freezing). It is an area affect attack, and lasts for a minute. Units under its effect are succeptable to infection. This is one of the only ways Flood can infect aerial units. When used on Flood enemies, it is still an area affect attack, but instead of freezing the enemy Flood, it merely converts them into friendly units.
Now, a lot of you will argue that the Flood become too powerful in the later game. But, please do not forget that they are also very weak in the early game, and more importantly, the Flood's pace is set by the other players. A wise player doesn't rush the Flood, but rather focuses on defense. When raiding the Flood, a wise player uses mechanized units that can fire and move at the same time, and makes sure to watch vigilantly, lest the vehicle stop for the brief second it would take to infect. Because players have to carefully watch their vehicles when raiding a Flood base, the player should make raids short. Because the resource gathering units are likely infantry-type units, they are succeptable to Flood infection, which thus makes the Flood a great economy killer in the early game.
And in the late game, the Flood will have its weaknesses. Turret Forms and Juggernauts, while useful, won't be an even match for a coordinated air strike. The Scarab would wreak havok on the Flood. Its height causes it to act like an air unit, and its power allows it to decimate enemy forces. Even Dominate Will will not truly stop a Scarab, since it won't wilt just because the operators inside are incapacitated. Juggernauts will most likely be required to take out a leg before a Scarab can be infected. It would be tough, but woe to any foe facing an infected Scarab.
That is really the strong point of the Flood. Anything you can throw at the Flood, they can take and throw back. Thus, the enemy players set the pace.
Strong Against Flood: Hunters, Warthogs, Spectres, Air Units, Scarabs
Weak Against Flood: Infantry, Slow Ground Vehicles