You are dropped off at a dark swamp with an Assault Rifle, a Pistol, and full grenades. You should see another Pelican in the distance, just off to your left. Walk to it. If you're playing on easy mode you should find two shotguns and plenty of ammo for them nearby. You don't need to grab one, but it is highly recommended. On any level, there are three Assault Rifles (one is on top of the weird-mushroom things behind the Pelican). Picking extra AR ammo up is also highly recommended. Head out into the swamp, away from the back of the Pelican. Some Grunts and Jackals will appear. These two types of enemies will be the only one's you will be seeing for a while. Kill them. After that try looking around for a Covenant Dropship lying against some rocks. Go around or through it and you should find some more Covenant.
After you take them out, you should see an enormous root-like thing with an Assault Rifle at its base. It's a bridge, so go across it. If you fall off, just circle back to the Pelican and try again (there won't be any more Covies this time around, so it should be a little easier). Upon crossing, you should see a stationary gun to your right and strange shapes in the fog. Climb either to where the gun is or to the left. You will be greeted with the sight of some Grunts and Jackals running for their lives, a torrent assault rifle fire, and an explosion which flips the stationary gun below when you come closer. Ignore all of that (Covie's included) and continue on. Even if you are spotted by them, you can simply run inside the structure, which they won't follow you into. No surprise, as they just ran out of it.
Inside, you should see a lift. Go down. Straight in front of you is where you need to go. The wall you see is open on either the left or right sides, but there's a large amount of Covenant soldiers blocking it. Clear them out with a grenade, then finish the stragglers. Go through the door and you should find some more Covenant; still the usual Grunt and Jackal combination. Kill the ones on the platform you are on, then either snipe the ones below or jump down and finish them. The door near the Covenant is where you need to go. Note that the doors on this level with green lights will open for you. Going through the door, you run into a wall. Go either left or right.
The door that opens will lead you to a large room with a strange structure in the middle. Go to the left. More Jackals guard a door. Stick one with a plasma grenade (if you haven't alerted them yet) and kill the survivors. Continue on through the next couple rooms, always entering doors with the green lights on them. If you can't find any on the floor you're on, try looking up on the level above you, as most of the rooms have two levels. Eventually, after passing through a large room with two plasma turrets, the next door you come to will put you directly in front of a crazy marine with a pistol, babbling stuff. He will shoot at you, but just stay out of his way. He won't follow you. If you want to hear what he's saying, you can just stand behind the pillar or wall thing he's backed up against.
You should find some weapons lying around here, usually Covenant plasma weapons. After you're done, head to the back of the room (opposite where the Marine is) and jump onto the platform above the fire. Run around to the door on the other end (the one with the Marine) and go through. This is another good place to hear the Marine's ranting. Through the door and the hallway beyond is a light bridge. You can either activate it or go around the platform sides to the door at the other end. There is an Assault Rifle on the floor. Go in the door. Go to either the right or left (doesn't matter, they both end up in the same place). The left path has an Assault Rifle and a med kit, if you need either. Walk down the ramps to the door below.
A cutscene will start, showing the introduction of a new threat
The Flood[edit]
After the cut scene, go to your left if you need ammo or weapons, then go to the door opposite where you start from. Wait for the same monstrosities from the cutscene to break it down. These are Infection Forms, the first stage in the horror that is the Flood (as in the chapter title). They aren't very strong (they only do minor damage and a single round from any weapon will pop them along with a few that are close, with the potential to cause a chain-reaction), but there are a whole lot of them. Once they break down the door, throw a grenade into their midst (be careful with Plasma Grenades, as you might tag one and get it in your face). Kill any survivors with normal weapons fire. The rest of the rooms will now burst open. The mass will show up on your motion tracker, so you can see where they will be coming from. After all the doors to your sides open, the one behind you (the door you came through) will open as well. This time, in addition to the Infection Forms, something new and a lot more dangerous will attack you. The hulking, bipedal Elite-looking monstrosities are called Combat Forms. They're made from Elites taken over by the Infection Forms, and are nasty customers, with insane jumping skills, a stinging tentacle-assisted whipping melee attack, and a serious case of not knowing when to stay down. On lower difficulties, you can use the Assault Rifle to knock them down easily enough, but on higher levels it's suggested you stick to covenant plasma weaponry, pistols, and, of course, the shotgun.
After destroying the Flood in the room, go out the now-open door. Head up either ramp, but beware: more Flood await. Go out the door you came in before the cutscene. Out in the area where you were earlier, Covies and Flood duke it out. The Flood usually win this one, so you can either wait until they are all dead and finish the Flood, or throw grenades in and hopefully kill most enemies (it is advisable to turn off the light bridge if you decide to do this). After killing the last offender, jump down. There's no point in trying to find the lift you came down. If you do find it and activate it, it'll come crashing down. Ignore it. Instead, head out to the only open door on this floor. If you don't really want to fight either group (which can be a drain on your ammo), simply leave the light bridge on and run across to the door on the other side – it's open. Go inside, and move through the halls in a reverse of the way you came in. If there are any Flood in your way, blast them. Some of the doors that you came through are locked now, so look for more open ones. Often times this means literally open, as in the doors the Flood have busted through.
Along the way, you will find some surviving Covenant (yet more Grunts and Jackals) and, on lower difficulties, more shotguns. Eventually, you will reach a lift. Activate it, and you will go down to a lower level. Here you run into a new modification of the Combat Form. They can apparently wield weapons, and they do so without hesitation. Most of the Combat Forms from now on will be packing heat, UNSC or Covie. But this is really a blessing in disguise. When they die, you get all their ammo. And there tend to be a lot of Flood around you. Basically, when fighting the flood, you either have full ammo or almost none. Also, you will run into Combat Forms made from marines. While they look weaker, they actually have the same health. Treat them as you would an Elite Combat Form: as a threat, and with a hail of lead.
Once you have killed the Combat Forms in this room, jump up the Covenant crates blocking one side of the door out. On top is an Overshield. Get it, then continue through the door. You will find a pair of Active Camos (which are effectively useless against the Flood, as they are extremely resistant to melee attacks, and can't be killed with a hit to the back) a malfunctioning light bridge, and some surviving marines. You can try and save the marines, but it's pretty much impossible. A single Infection Form will kill them. Just kill them all. When you're done, go out the open door. Again, continue through the rooms. There will be more Flood. Some of the halls you move through will have busted doors that lead to rooms with Combat Forms in them. You can hide in these, but it isn't recommended. If you get trapped, there's no way out.
Finally, you will reach a room with a light bridge. Activate it, and run across, but be ready to fight. A horde of Flood will charge your position from the room on the other side. Charge them and thin their numbers with grenades. After fighting your way through, start the lift you find there. This will lead you up to a group of marines, as well as put you back in touch with Echo 419 (the Pelican dropship that put you in this swamp in the beginning of the level).
Basically, follow 419's directions to the structure where you will get picked up. If you can, try and save the marines, but it's not required, and not recommended on higher difficulties. They just don't last that long, and protecting them costs you ammo you're going to need later. When you do reach the structure, run straight up to it (blowing away any Flood that rush you) and trigger the arrival of a some new faces. These floating robots (called Sentinels) will assist you in killing the Flood. Just keep killing until the cutscene starts, where you meet 343 Guilty Spark, who transports you to the library.