From Halopedia, the Halo wiki
Go through the door and you'll see a Grunt being chased by an unarmed Elite combat form. Kill them both with your assault rifle. Go to the dead end. If you look to your left, where the Grunt and the combat form chasing him came from - there is an Active Camouflage there. Go right then at the opening left. You should see four Grunts. Throw a Fragmentation Grenade. Then go to where they were and go left. There will be two combat forms. Swap your plasma pistol for the shotgun, and go straight to the dead end then right. Take out the Carrier form and its infection forms. Go through the door and jump through the gap. From this point on, Shotgun Ammo and Grenades will be your most important resource.
When you jump, there will be large fight between Covenant forces and Flood. Throw one grenade at the Elites, and pull out your shotgun if you have not already. When the Flood comes out of the coolant, use your shotgun to take them out. Go where the Elites came from (turn on your flashlight) and go right and continue going to straight into the next area.
Now, when you find the path, go through it and you'll find another group of Covenant and Flood battling it out. It is recommended to watch the fight, as they can easily kill many of each others' forces. Once it is over, go straight to the other side. There's another path you need to go.
Enter the path and take out your shotgun. There will be lots of combat forms here, so be prepared. Take them out carefully. Also, watch out for the falling Carriers. Don't worry if there are lots of Flood behind you. However, if you are playing on Legendary, you will need to take them out as quickly as possible.
Now once you got to the other side, there is a health pack and a Sniper Rifle. Swap your primary weapon (not the shotgun) for it. Then, stay where you are. There are Hunters fighting Carrier forms in the next area. It's simple, you need to aim at the orange part at the back. When you finally get a hold of it, simply snipe it.
Once the Hunters are defeated, aim and kill the remaining Covenant. Then swap the sniper for the pistol. Jump from the small cliff and if there are Covenant still then you need to kill them. Another way is to kill the Elites and Grunts first, while leave the Hunters to deal with the Flood, since Hunters are often occupied with battling Infection Forms and will not engage you.
On the other side, there is an Elite on a Shade and a couple of Grunts. You can do one of two things here:
1. You can take them out with grenades.
2. Let the Flood take them out.
Once the area is clear, go left and right again. There will be several Flood forms here. Use your shotgun to take them out. If you haven't already, you should swap your Sniper Rifle for a Pistol, and continue on going straight. Drop down the cliff edge.
Upon going straight, you'll encounter Grunts fighting. Throw a grenade and stick one of the Combat forms. By this time, your shotgun, if you haven't been scouting the area for ammunition, is either low on ammunition or completely out. Snipe the enemies on the higher level with your pistol and go straight to where the combat forms came from and head left. Follow the path and you'll notice Elites fighting Combat forms on the higher ledge, along with an overshield. Grab it and kill the Combat forms with your pistol. One of them should have a shotgun, so grab it. Keep your pistol, though.
Also, kill the Carriers and head up to the higher ledge, kill the Elites, and a cutscene will happen in 5–10 seconds.
After the cutscene, you're inside the ship. Turn around and head toward the open door. Follow the path and kill the carrier form with your shotgun. If you still have your pistol, move down the path and you'll be in a large room patrolled by Flood carriers. If you go down your current level, there's two Combat forms with pistols and shotgun ammo. Kill them both with your weapon. Then, grab some ammo and go down the lower pit.
If you have good skill, you should be able to kill the carrier forms, ignore the Flood reinforcements, and enter the door opened from the right side. Pull out your shotgun and kill the enemies, and collect any ammunition they have. Find the hole and enter it. There should be a carrier form, but don't worry, as it would probably miss.
Then, follow the path and kill the two Carrier forms and its surroundings. Continue to go straight then left and you'll have two Elites and a couple of Grunts. Stick the Elites before they kill you. and then go right and left again and kill Grunts, Elites and Flood and quickly go right and left then right again and you'll be in the shuttle bay.
If you need health there is a health pack next to the door you came through.
Go straight on your current level, and turn right (don't enter the door) then continue moving to the end of the level (ignore the Elites) and there is a door open to your left. Enter it (also, if there are Elites chasing you, stick them).
Now follow the path and you'll find several grunts fleeing, Kill them and the Flood chasing them. Follow the remaining path, killing every enemy you encounter with your weapons until you head towards the third level. Continue getting ammo also.
Once headed into the third level, (use the health pack, if needed) then enter the door and go right. There are a couple of Flood forms, so throw a grenade or two. Enter the door they came out of (ignore the Elites and the dropship) and also throw another grenade. Then go straight to the dead end and left, go through the door and right.
Go straight and you will see Elites fighting. Stick one of them before they see you. Then, go left throw a grenade and clear the area filled with Flood. Push toward the command center; the Flood will keep coming out until you enter.
Once you are in the command center of the ship, head for the Proto-Gravemind. A cutscene will activate.
Once the cutscene is over, get off the platform and wait a few seconds. Flood forms will come in through the doors. Head for the door that you came through and get close enough to open it; but do not go through. It will open, revealing a large group of Special Operations Covenant. Watch the huge battle erupt between the Covenant and the Flood. If you have any grenades, throw one in every once in a while to even out the fight. Once it is over, and the area is secure, go through the door the SpecOps enemies came in, and go right.
You can punch through Special Operations Covenant by leaping through it but it's not reccomended on Legendary and quickly escapes as the Special Operations will focus on battling the Flood inside Control Room rather than you. Throw grenade as a distraction when leaping so they have less time focusing on you.
Go back to the shuttle bay. There, you will face several more Special Operations Covenant enemies. Stick the Elites before they kill you. Then go back down to where the Elites were (the entrance to where you came in to the third level) and go down and left. There are Elites and a Grunt. One grenade will do.
Go to the path they came in and also, there are three SpecOps grunts that are blocking your entrance. Kill them (also, you might want to stay away from the Fuel Rod Guns until they explode; they will set off any nearby grenades). Then, move on to the next area.
Now kill the Minor Grunt you see there. Then go to the other side of the shuttle bay and drop from the bottom, you should only lose half shields so don't worry. Now quickly enter one of the escort Banshees to finish the level.