Part 1: Under New Management
After teleporting, switch to your Plasma Pistol and move forward, there will be a caged wall on the left side of the current hallway. Captain Jacob Keyes can be heard saying "Chief, don't be a fool. Leave me!", if you looked well you will see a Proto-Gravemind, that is what Keyes transformed into. Grab your Plasma Pistol and head to the end of the hallway and walk through the door. You will see a Grunt fleeing from a Flood Fighter, wait until they go away and turn left. Grab the Active Camouflage and head to the end off the hallway. You will see a group of Grunts shooting a bunch of Floods. You can either wait for more bodies to fall or simply through a frag grenade. If you did it right they should all die, now move on and keep your Plasma Pistol equipped, the Shotgun on the floor is low on ammo anyway. Take out the exploding Carrier Flood at the end of the hallway and walk through the next door, and jump through the hole in the ship. If you stayed for a while, a massive amount of Flood waves will dash in.
After jumping through the hole take out the Covenants and Floods in front of you, after that turn left and swap your Plasma Pistol with the Plasma Rifle, a couple of Floods will drop from the shop, just take them out. Move through the next chasm and through the dead Covenants bodies, you will see another combat taking place between Floods and Covenants. Take out the Fighters on the right cliffs first, then take out the remaining Covenants, Now move to the next chasm. If you stayed a lot of spores will drop into the fuel lake and attack so just simply move on. Another wave of Fighter Floods will dash in, take them out with the Assault Rifle. Now keep moving through the chasm and be real cautious since a suicidal exploding Flood Carrier will drop, step back and shoot the spores after it blasts. After few feet another one will drop with other two Fighters armed with weapons, take out the Fighters and finish off the Spores. If your Assault Rifle is low on ammo or already ran out of it, then swap it for the Pistol which has over 60 rounds. Next you will find a health pack and a Sniper Rifle on the ground, ignore the sniper since your pistol already got one. After reaching another area with fuel lake, snipe out the Hunters first using your pistol.Then try sniping as much targets as you can before getting down, you don't have to worry about drowning in the fuel, the armor will prevent it. Next, slide down and move to the battle ground, finish the remaining Covenants or Floods and resupply. It is preferred to have a Pistol and a Plasma Rifle at this point, so swap for Plasma Rifle's ammo and move on. A location point will be displayed on your hud.
After reaching a checkpoint trun slowly on the chasm's corner, you will see a Grunt next to Shade Turret occupied by an Elite. Bring up your pistol, zoom in and snipe out the Elite on the turret then take out the Grunts. Floods will soon arrive, use the Pistol's sniper for your advantage but don't go shooting out the whole bullet rounds. Then switch to your Plasma Rifle and take out the Flood fighters, face more Floods with your Pistol if you felt surrounded and keep your grenades for now. Move up a ramp into an arched wall and shoot the couple of Fighters charging toward you, notice that you can simply "stomp" on the spores but it will reduce a slight amount from your Energy Shield. Jump from the edge of the arched wall and move along the chasm to combat area, again take out the Floods first then take out the Covenants. There should be an Assault Rifle around, swap it for the Plasma Rifles and snipe out the Floods above you with the Pistol. Move to the Next chasm and into the Gravity Lift. You will have to hold your position until it re-activates, turn your sight back and take out the spores. Then turn back again to the Gravity Lift and pick up the Overshield beside the Fuel Lake, take out the remaining foes around the Gravity Lift using the Pistol on the Fighters and Covenants, and a spray from the Assault Rifle at the spores. Now get into the Gravity Lift and avoid unnecessary combat with the new waves of Flood Fighters.
 Part 2: Upstairs, DownstairsAfter reaching the cruiser, take out the spores on board using your Assault Rifle. There will be two open doors in the current room, one that holds a locked room and another one with a way to proceed to, it is the one opposite to the burning door. Walk through the hallways of the ship it is pretty linear, then when you reach the hallway where a Flood Carrier is charging in, turn back to take out the one behind you. Then finish off the other, he might be exploded by now, again take out remaining spores. Move along the hallway with more dead bodies on the ground, walk through the last door into a two-story room that holds a Wraith in it. Use your Pistol again to snipe out the Carriers and the Fighter on the ground level, then quickly switch to the rifle and take out the Fighter charging towards you. Get to the door at the end of the upper level and make your way down. Don't bother at any time to snipe spores, it is really pointless. As you walk through the last door that leads you to the first floor, a wave of Fighter Floods form will charge through. Take them out and use Grenades wisely. Take out any remaining spores in the next room and ignore the Ghosts, you can't ride them, and go to the next hallway. You will notice the absence of any Covenant life form, the Floods are taking over, take out the new wave of Floods and take it easy on the Pistol, use the rifle when facing a large number of Fighters. Move right and drop from the hole in the floor, step back and shoot the Floods in the current room. There will be a couple of Elites at the end of the hallway, take them out and pick up the Pistol ammo. Move around and another massive wave of Flood fighters will arrive from the ceilings, switch to your pistol it is really effective against Fighter Flood Forms. After finish them off, get to the next room and into the Shuttle Bay.
In the shuttle bay, get behind the pillar in front of you and use it as a cover, snipe the group of Elites on the Shade Turret on the opposite side. Now make your way to the Shade turret and get on it, a large amount of Elites and Floods will charge, take them all at once. Be real careful not to fall down to the ground level, you don't really want to do that. Next, get to the hallway entrance at the last corner of the current area. The hallway will be crowded with Grunts and Floods, so the use of grenades here is extremely helpful. The music should give you a hint, because when it stops playing, it indicates that no more foes are present. Take out the couple of Floods nearby and make your way to the third level of the shuttle bay. Just on your left side you will see a door with Floods gathering in, toss a grenade and shoot the Fighters by the Pistol. Get in through that door when done and resupply. Walk through the hallway and into the checkpoint.
 Part 3: The Captain
Walk through the door and clear out the hallway from the waves of Floods, there are three doors that are active, but only one that really leads somewhere. Get in the next room to find a large Brain Form Flood, Captain Jacob Keyes turned into a Proto-Gravemind. Don't worry, you won't really face or engage in combat with it, walk to it to trigger a cutscene. After watching the cutscene Honour Guards Elites and Grunts wielding fuel rods guns. Take them all out and proceed to the shuttle bay. Take out the SpecOps Grunts and Elites in the Shuttle bay and wait for the Covenant air units to land. Toss a grenade to eliminate an Elite or two, then jump over the bridge that holds the Shade turret and into the ground level. You can either engage in combat with the Covenants or simply get in the Banshee and fly it to the exit of the Shuttle Bay. Next to The Maw.
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