After fixing the reactor core, Adam tells you to investigate the massive damage in sector 5.
Go to Sector 5
Uplink for your next briefing. Even more damage has been done, by a creature in the station known by the researchers as the Nightmare, a bio-mechanical organism created for military applications with the ability to manipulate gravity. It has likely become an X host. You are to find and kill it.
Exit right through the Save and Recharge Rooms. You'll have to jump to avoid the energy ball thrown out by the crab-like thing below. Drop to the bottom of the shaft and go through the yellow hatch to the right, then exit right once more, to the big room where you saw the scary shadow flying past in the background (which, as we know now, was the Nightmare). The room is in bad shape from the damage caused by the Nightmare.
Space Jump to the top left door, open it, but don't go through. Instead, kill all the Chute Leeches to the right and get to the right wall. Make a running start towards the left, and once you reach the gap, crouch to hold the Boost energy. Hit A then tap left when you float up, to Shoulder Charge through the door to the left. You will break through some Boost Blocks in the next room to reach a Power Bomb tank. Go back out to the big damaged room.
Fall to the bottom of the room. Go all the way right and through the damaged door to the right. The sub-zero environment has dissipated due to the damage caused by Nightmare. Continue through the broken door to the right, which used to be a red hatch. Shoot the ceiling here to open it up, and jump up. Get on the ledge by the door and drop a Power Bomb, and a small hole will appear above the door, leading to an area above. Be careful; there are Space Pirates above. Jump up, pull up and quickly drop a Power Bomb to kill the Space Pirates and break open some blocks above. Climb up and kill the Space Pirate that appeared up here, then shoot the ceiling to the right to open the way further up. Space Jump up there and open the gate, then fall back below. Shoot the ceiling to the left now and Space Jump up again, opening the second gate. In the area that was blocked by the gates, drop a bomb to the right to open a block, drop another bomb where it was, and bomb to the left to reveal a Power Bomb Tank. Allow yourself to fall through the Pit Block, then return to the very bottom of this long shaft (the door on the way leads to a neat-looking tunnel to Sector 3, which you don't want to go through). Down at the bottom, exit right, then exit right a second time.
Kill all of the Gerutas in here; if you're lucky, one will release a red X. Make your way right, and exit right. Bomb the floor in the next room to fall into the water below. Avoid the enemies and exit right (you may not be able to avoid the beams from the Space Pirate at the bottom).
In the next room, if any free-floating X join with a Space Pirate, it is morphed into an aquatic creature. Head right, and instead of going through the door here, jump to the ledge above and exit through the door to the left. Make your way up to the door above and go through.
Get rid of the Geruta and shoot the ceiling to open it. Jump above and exit through the door on the left. Use a Power Bomb to kill the Zeela; a Power Bomb tank will be revealed. Grab it. Keep returning to this room if you wish, killing the Zeela with Power Bombs to replenish your energy and weapons. Exit the room.
Make your way to the right, then jump onto the ledge you see where there is a door above. Use a Power Bomb to reveal a tunnel to the left, across from the door. Pull into it and roll to the left while bouncing until you discover a hidden passage. Roll into it and bomb the left side to reveal a Power Bomb Tank. The door here leads to a Recharge Room, so use it and go back out. Lay a regular bomb in the gap to reopen the tunnel, roll through and use the door at the end to reach a Save Room. Save, exit, drop below and go through the door to the right.
Kill the Zeela on the way and Space Jump up when you can, to reach a Living Door on the door. Kill it, collect the red X, and go through. Don't go straight for the Energy Tank or you will fall below to the Nightmare's room. Instead, drop a Power Bomb to reveal a tunnel above for the correct path to the Tank. Roll through and get the tank, then roll to the left to fall below to the Nightmare's room.
This is a notoriously tough boss. Therefore the strategy will be long. You'll probably have to try multiple times before you kill it.
In the first phase, its vulnerable point is the round thing underneath it between its arms, which can be hurt with Missiles or charged shots.
It will shoot an array of beams from its arms. If the Nightmare is near the ground, you'll have to jump over the beams, but this will make the Nightmare float up towards the ceiling, allowing you to run below it and shoot Missiles straight up at the thing underneath it.
If the Nightmare floats a little higher, the beams may pass over your head, so be careful not to jump and get hit by them. Allow the Nightmare to float close to the ground before jumping over the beams.
When you do jump the beams, jump as high as you can to make the Nightmare float high enough in the air that you have time to shoot Missiles at the underside.
After hitting it with a few Missiles, the round vulnerable part activates and the gravity in the room is made stronger, so you move as if underwater. You have to be careful during this phase to jump soon enough to clear the beams shot by the Nightmare.
Also, your Missiles will be drawn to the floor by the gravity, so you will be unable to hurt the Nightmare with Missiles unless it comes very close to you (which you don't want to happen). Use charged shots at this point.
Duck any beams shot above you. Your jumping will not affect where the Nightmare floats at this point, so don't bother trying to jump as high as possible. Jump over beams near the floor. Jump before you think you need to, because you're moving slower.
Instead of jumping to make the Nightmare move, just wait for it to hover high enough up in the air that you can run underneath and shoot a charged shot. You may want to stay close to its near arm so you can get under there quickly. Remember that you have the wide beam, so you don't have to run all the way under the vulnerable spot, just near enough that the beam hits it. This lets you get away from underneath more quickly.
The Nightmare will move back and forth toward you, so you'll have to stay out of its way.
Once you've hit the Nightmare enough times, the round vulnerable spot will flash, the gravity will go back to normal, and the Nightmare's faceplace comes off revealing an ugly, drooping face. Naturally this is its vulnerable spot, but you can't aim too high or too low or the Missile will bounce off. There's only a small vulnerable window.
When it first loses its faceplate, get on the ladder and start shooting its face with as many Missiles as you possibly can. Just tap B as fast as possible. The more you shoot, the shorter the battle will be. When it gets too close, carefully Space Jump over it to its right side.
When the Nightmare reaches the bottom left corner of the room, it will then start to chase you around the room. You'll have to Space Jump away from it as best you can. It can be tricky, so you might need to practice a while on this boss so you get better at it. Try your best not to let the Nightmare hit you. You can usually Space Jump in a circle around the room, but sometimes the Nightmare might start by cutting straight across to you, which is hard to avoid.
When you're on the left side of the screen, you want to lure the the Nightmare into a position where you'll be able to hit its face when it stops chasing you.
Eventually, when the Nightmare is on the right side of the room, it will stop chasing you and start to slowly hover towards the left wall. If you're lucky it will be in a position where you can hold onto the ladder and shoot a ton of Missiles into its face. Make sure you're shooting as fast as you can. The more you damage it, the fewer times you'll have to be chased around the room by it, which is probably the trickiest part.
If the the Nightmare is too high or too low to be shot, you should just give up and Space Jump or run to the right side of the screen and wait for it to reach the bottom left corner and start chasing you again.
With luck, this strategy will succeed and the the Nightmare will turn into a Core-X. Shoot it with your beam if you are in need of energy after the tough battle. As usual, hop over the Core when it moves towards you, shoot it with a Missile, and wait for it to stop flashing before shooting it again. Grab the Core-X that it releases to recover the Gravity Suit.
Sector 5 (ARC)
With the Gravity Suit, you will now be able to move normally in water without getting slowed down. This allows you to Space Jump and Speed Boost in water. You are also protected from lava now.
Get near the hatch to the left to open it, but don't go through yet. Instead, go to the far right wall, then make a running start towards the left and you'll break through some Boost Blocks in the next room. Exit left twice, drop below and exit through the door here.
Head to the right, fall down below the ledge, then head left and exit through the left door. If you Space Jump up you see a gap in the right wall. You want to try to Space Jump up and shoot the wall directly across the gap with a Missile. Once you've destroyed the Missile Block, Space Jump back up there and pull into the tunnel. Roll left to a new room.
As a ball, keep bouncing until you get through a hidden hole above to reach the Energy Tank. Go to the right to fall through some Pit Blocks, and exit the room through the narrow tunnel.
Drop back below, get the enemies out of the way, and exit right to the corridor with all the Space Pirates. Kill all the enemies in the bottom corridor, then from the door on the left make a running start towards the right, shooting your beam to open the door so you break through two walls of Boost Blocks in the next room. Right after you break through them, crouch to hold the Boost energy, then run back between where the walls were and press A to do a Hyper Jump through the Boost Blocks in the ceiling. Grab the Power Bomb Tank here, then walk to the left to fall through some Pit Blocks back below.
Go to the left side of the room and make a running start to the right, heading through the tunnel that leads to Sector 4.
Sector 4 (AQA)
You will Speed Boost; when you reach the end of the second ramp, jump to break through a wall of Boost Blocks above, opening the way to the door on the right. Exit through it to reach an underwater environment.
Exit right for a Save Room, then go back out. Go a little bit below to a door leading to the right. Go through. The Gravitts along the floor and ceiling are vulnerable to Missiles or charged shots. Break through the grey blocks as you head right to reach a Missile Tank at the far right. Grab it, then return to the aquatic shaft.
Go up to the wall to the left, and bounce as a ball against the wall to access a hidden tunnel leading to a Power Bomb Tank. Grab it and return to the shaft. Go all the way to the bottom and exit through the left door. The red hatch blocks the way at the left end, but use a Power Bomb in the yellow tunnel to reveal Missile Blocks. Shoot them and jump above. Jump on the ledge on the right and up to a new area. Shoot the top right (not the top left) to open a passage. Pull into it and bomb to the right to reach a Power Bomb Tank. Go back to the last enclosed area.
Shoot the air vent block at the top left and pull into the tunnel to a corridor leading left. Exit left. Use charged shots on the Evir, and head to the far left where two air vent blocks are in the floor. Bomb them and fall below. Go to the floor further down and bomb the second air vent block from the right to drop down. Plant a bomb where you land to drop down further. There is a hidden hole in the right wall, so shoot the Skultera through the hidden hole and roll as a ball through it. Bomb the grey block below, then fall down and bomb the grey block to the left that is blocking a Skultera. Kill it and you may notice your beam passing through the left wall. Roll through that wall and bomb the air vent block below, and you'll find yourself at the Level 4 Security console. Log into it to release the lock on red hatches, and exit through the red door on the right.
NOTE: There is a special secret scene you can see now that you've unlocked the red hatches. You need to do it before getting the next upgrade. It is extremely tricky, involving many Speed Boosts and Shoulder Charges to reach a Navigation Room. I have never tried it, so consult another Metroid Fusion walkthrough to find out how to do it.
Space Jump up until you see a gap in the right wall, across from a bunch of trapped Scizors. Land on it, then bounce as a ball against the right wall to roll into a hidden tunnel. Make your way to the bottom where there are a bunch of trapped Scizors. Lay a Power Bomb but get away from it, because you want the free-floating X from the Scizors to re-form into golden Scizors. Shoot the now-visible Missile Blocks and kill the Scizor(s) with two Ice Missiles. Now the hatch will unlock, so go through.
Get up above, and either lay a Power Bomb or just bomb your way through the air vent blocks to find a hidden Energy Tank. Once you've collected it, make your way out of the passage and exit. Make your way above to the hidden tunnel that brought you here and roll back through it. Space Jump to the top of the shaft and go through the red hatch at the top. Go right through two doors, to another room with thin walls and another yellow tunnel (not the first one you reach).
Kill the aquatic Space Pirate, then head right and set off a Power Bomb in the yellow tunnel to break open the floor. Get the Missile Tank from below, then return to the tunnel and exit right.
Make your way up this shaft, killing Skultera and Evir on the way, and exit through the red hatch above. Pass through the tunnel to the next room. Shoot the two air vent blocks next to each other in front of you, then pull into the passage and get to the other side. Go into the Save Room at the end, save, and come back out.
Jump onto the ledge above and continue left. Ignore the first puffer fish you see, and continue upwards. There will be a second puffer fish blocking your way, so get far enough away that it deflates, then freeze it with an Ice Missile so you can get past. Exit through the door beyond, then exit right once more.
Kill the Gravitts, then get as far right as you can just before the Kago. Make a running start to the left while shooting to get through two doors and break through some Boost Blocks in the floor. Exit through the door you reach.
Get rid of all the Gravitts, and notice a gap in the ceiling just before the door on the right. Head back towards the left and get up against the left door. Make a running start to the right. Crouch before hitting the door to the right, and do a Hyper Jump where the gap in the ceiling is to break through some Boost Blocks in the room above and reach a Power Bomb Tank. Get it. Then, you'll want to start falling down the passage that you jumped up through, pressing against the left wall to grab a ledge below the top ledge. Pull up into it and go through to reach a Missile Tank. Roll back through the tunnel and fall to the corridor below. Exit through the door on the right.
Space Jump quickly to the topmost ladder (above the water level) so you get there before the puffer fish form. From the ladder, shoot a Missile up at the block in the way to break it open, and jump up to the ledge above. Go through the door here.
Use a Power Bomb to kill the Owtches and open the way. Go through the red hatch. Drop below and go through the red hatch here to access the Data Room. Download the Diffusion Missile data. Now, you can hold R to charge up your Missiles so that when they hit something, they will diffuse and freeze surrounding enemies. Exit the Data Room.
Standing by the door, charge up a Diffusion Missile and fire it at the wall to freeze all the puffer fish while they are still deflated. Roll through any of the now-unblocked tunnels, and continue left through some grates on the bottom floor. Destroy the purple barrier and continue left. Roll into a ball just before the wires, and bomb the wall below them to reveal a Missile Tank. Grab it, then open the gate and return to the last room.
Climb the ladder to the door and go through. Jump up and over the wall to the left to the door, and go through it, and go through the next door as well. Drop a bomb against the bottom left corner to open a tunnel. Roll to the end and drop a bomb to fall below. Use a Power Bomb at the bottom to reveal tunnel at the left leading to a Power Bomb Tank. Get it, and jump back up the platforms, pull into the tunnel above, bomb the block at the end, and exit right twice. Make your way to the Navigation Room for a new briefing.
Adam will be surprised you got the Missile upgrade, since HQ didn't send word of it. Adam chides you for unlocking the Level 4 hatches, and orders you to use more discretion from now on.
The X seem to have infected the rogue Security Robot you faced back in PYR. It is now in Sector 6. Head to Sector 6.