After you fix the reactor core, Adam tells you to investigate the massive damage in sector 5.

Go to Sector 5

In the Sector 5 Navigation Room, Adam tells you to find and kill the Nightmare.

Go to the right, through the Save and Recharge rooms. When you arrive in the next room, jump to avoid the projectile that the Zeela shoots in your direction. Go down to the bottom of this tall room and go through the door on the right. In this small room, go through the door to the right.

Space Jump to the top left door, then open it without going through. Go to the right and kill all of the Chute Leeches on the floor. Go to the far right, then run to the left. Crouch at the end of the path, and if the door to the left isn't open, shoot it open, then jump to float, then press left to do a Shinespark through the door to the left. You will break through some Boost Blocks and reach a Power Bomb tank. After you get it, go back to the large room.

Go to the bottom of the large room, then go to the right, killing the Chute Leech on the floor as you go. Go through the bottom right door of the large area.

This is where the sub-zero environment used to be. Go through the upper right door. Shoot the ceiling to open a hole. Jump up through it, then stand near the door and drop a Power Bomb. Jump straight up to find a hole in the ceiling above the door. Jump up through that hole, then either shoot the red light and quickly kill the Space Pirates, or drop a Power Bomb to kill them. Then shoot the left side of the ceiling and jump up to kill the Space Pirate there. Shoot the left side of the ceiling and the right side of the ceiling to open holes there, then Space Jump up there to shoot the red lights to open the two gates. Go through the hole in the left side of the ceiling and go to the right, and shoot the floor in the corner to open a hole. Keep shooting and bombing your way farther into the hole to get a Power Bomb tank. Fall through the Pit Block below where the tank was, then go to the bottom of this room, and go through the door on the right. In the room with the hole in the floor, go through the upper right door.

Kill the Gerutas in this room. One of them might drop a red X. Go to the right side of this corridor and go through the door on the right. Shoot the floor in this room, then stand where the floor disappeared to fall through some Pit Blocks. You will fall into some water. At the bottom, kill or avoid the Space Pirate, then go through the door on the right.

In the next room, free-floating X can combine with Space Pirates to turn them into Aqua Zebesians that can swim quickly. Go to the right, but don't go through the door. Instead, jump to the ledge above the door and go to the left. Go through the door on the left. Then kill the Aqua Zebesian and make your way to the top of this room. Go through the door there.

Kill the Geruta on the ceiling, then shoot the ceiling to open a hole. Jump up through the hole, then go through the door on the left. Drop a Power Bomb to reveal a Power Bomb tank in the bottom left part of the room. Take it, then go back to the previous room.

Go to the right, then go up to the upper right corner of this room, where there is an undamaged door. Don't go through it. Instead, drop a Power Bomb to reveal a tunnel to the left. Roll through it while jumping. You will find a hidden passage above the tunnel, slightly to the left of the center of the tunnel. Roll to the left in the upper tunnel and drop a bomb at the end to reveal a Power Bomb tank. Take it. You can go into the nearby door to find a Recharge Room. After you leave the Recharge Room, go to the right and roll into the niche in the wall and drop a bomb there to reopen the tunnel. Roll through it and go through the door to the right to find a Save Room. After you leave the Save Room, go downward to the damaged door on the right. Go through it.

In the room with all the Zeela, go to the right until you can Space Jump up through a hole in the ceiling. In the upper area, you find a Living Door. Kill it, absorb the red X that it drops, then go through. Don't go directly toward the Energy Tank or you will fall through some Pit Blocks to the boss's room. Instead, use a Power Bomb, or drop a normal bomb against the hanging wall in the upper center of the room to reveal a tunnel. Go through it and you will fall through some Pit Blocks at the end to get the Energy Tank. Go to the left from there to fall through some Pit Blocks into the Nightmare's room.

The Nightmare

In the first phase of the battle, use charged shots or Missiles to hit the glowing round thing between its arms. Nightmare will shoot beams toward you from its arms. Jump upward to make Nightmare float up, allowing you to shoot the glowing thing between Nightmare's arms. Be sure to jump as high as possible to give yourself plenty of time to shoot Nightmare's weak spot. When Nightmare floats up, be sure not to jump upward into the oncoming beams from its arms.

After you have done enough damage, Nightmare uses its gravity manipulation device to weigh you down. You will move slowly, as if you are in water. Missiles will fall to the floor, so you must use charged shots to continue hitting Nightmare's weak spot. When jumping over Nightmare's beams, be sure to jump as early as possible so you have enough time to avoid the beams, and duck any beams that are shot above you. Jumping will not change Nightmare's position during this phase of battle, so just run in and shoot a charged shot whenever Nightmare floats high enough. Stay near Nightmare's arm so you do not have to run far. You don't have to run all the way underneath because your Wide Beam will be able to hit Nightmare's weak point when shot at an angle. Keep moving to avoid Nightmare as it floats around and shoots its beams.

After this phase, Nightmare's gravity manipulator will fail, so you can move normally again. Nightmare's faceplace will come off, revealing its organic components. Its face is now its vulnerable spot. You have to aim carefully, because missiles will bounce off if you don't shoot directly into the face.

First, jump onto the ladder on the left side of the room and rapidly shoot as many missile as you can. When Nightmare gets too close, Space Jump away from it.

When the Nightmare reaches the bottom left corner of the room, it will start floating around, chasing you. Space Jump away from it, and shoot it in the face if you can. When it stops chasing you and starts floating toward the left, shoot its face as many times as you can.

After you have done enough damage, Nightmare will finally turn into a Core-X. Shoot it with your beam to release free-floating X, and shoot it with Missiles to damage it. After that, take the Core-X to get the Gravity Suit.

Sector 5 (ARC)

The Gravity Suit allows you to move normally in water without being slowed down, so you can now Space Jump and Speed Boost in water. You can also safely enter lava without taking damage or being slowed down.

Before leaving Nightmare's room, approach the hatch to make it open, then go to the right side of the room and run to the left. You will break through some Boost Blocks in the next room. Go through the door on the left, then go to the left and go through the door on the left. In this room, go down into the water and go through the door at the bottom.

Go to the right and fall down to the lower area. Go to the left and go through the door there. Then Space Jump upward until you see a small niche in the right wall. There is a Missile Block in the left wall, directly across from that niche. If you are having trouble finding it, roll into a ball in that niche and drop a Power Bomb. Shoot the Missile Block, then Space Jump to the tunnel beyond the Missile Block. Roll through it to reach a new room.

Roll into a ball and go toward the left while bouncing. There is a hidden hole in the upper left part of the thin floor in the upper part of the room. After you go through that hole, bounce to the right as a ball to avoid the Pit Blocks to the right. Bounce into the upper right tunnel to get the Energy Tank, then roll to the right to fall through a Pit Block and leave the room.

Go back down to the bottom of this room and go through the door on the right. Kill all of the Skultera and Space Pirates, then go to the far left side of this room and run to the right while shooting. You will go through two walls of Boost Blocks in the next room. As soon as you break through both walls, crouch, then walk to the spot between where the two walls were, and jump to do a Shinespark through the ceiling. Take the Power Bomb tank, then walk to the left to fall through some Pit Blocks.

From here, go to the far left side of the room and then run to the right. You will go through a tunnel into Sector 4. When you reach the end of the second ramp, jump to break through a wall of Boost Blocks up above, then go through the door on the right.

Sector 4 (AQA)

Go through the upper right door to find a Save Room. After you leave the Save Room, go downward and go through the door on the right. You can use Missiles or charged shots to kill the Gravitts on the floor and ceiling of this room. Go to the right, shooting through the grey blocks as you go. There is a red Zeela in an enclosed area near the right side of the room. Kill it to get a red X. At the far right of this room, there is a Missile Tank. Take it, then go to the left and leave this room.

Go to the left wall, and jump as a ball against the left wall. You will roll through a hidden tunnel to get a Power Bomb tank. Take it and return to the previous room. Go all the way to the bottom of this tall room and go through the door on the left. In the glass tunnel in this room, bomb the ceiling on the left side to break some blocks in the ceiling, then shoot a missile through the hole to open a path above the glass tunnel. Jump up through the hole and go to the right side, then jump upward to reach another area. The Evirs will shoot spiralling projectiles as they float around. They are vulnerable to Missiles and charged shots. Shoot the upper right corner of the right wall to open a hole. Roll into it and bomb your way to the right to get a Power Bomb tank.

Roll back through the tunnel and go to the upper left of this area. Roll through the upper left tunnel and bomb the block in the way, then go to the left to reach a new room.

Go to the far left of this room and bomb the air vents in the floor. Fall down through the hole, then in the area below, bomb the second air vent from the right. Go down the hole, then drop a bomb where you land. Go down the hole. There is a hidden tunnel to the right. Shoot Missiles or charged shots to the right to kill the Skultera, then roll into a ball and roll through the hidden tunnel to reach the are where the Skultera was. Bomb the grey block in the floor here, then go down and bomb the grey block on the left. Kill the Skultera and roll through the hidden tunnel to the left, then bomb the air vent below and fall through. You will reach the Level 4 Security Console. Use it to unlock Level 4 hatches. Then go through the door on the right.

NOTE: Now that you have unlocked the red hatches, you can attempt to see a secret cutscene. If you want to see the scene, you have to do so before you get the next upgrade. It is very difficult and involves Speed Boosting and maintaining the Speed Boost through several rooms by Shinesparking. Here is an image from Metroid-Database.com that explains how to do it.

From the room to the right of the Security Room, Space Jump upward until you see a niche in the right wall, across from an enclosed area that contains some trapped Scizors. Land in the niche in the right wall, then bounce as a ball against the right wall to roll into a hidden tunnel. In the next room, go to the bottom of the area and use a Power Bomb, but don't stay near the Power Bomb. This will allow the free-floating X from the Scizors to transform into golden Scizors. Shoot the Missile Blocks and kill the Scizors with Missiles. This will unlock the hatch in the bottom right part of the room.

Go to the upper area and bomb the air vent, then roll through the path, bombing air vents as you go, to find a hidden Energy Tank. Take it, then leave this room. Go back to the hidden tunnel across from the enclosed area full of Scizors. Space Jump to the top of this room and go through the door on the right.

This is the room where you can start the attempt to see the secret cutscene. Here is an image that explains how to do it.

If you are not going to try to see the cutscene, then go to the right and go through the door. In the next room, go through the door on the right. Kill the aquatic Space Pirate, then go to the right and use a Power Bomb in the glass tunnel to break a hole in the floor. Go down through the hole and take the Missile Tank, then Space Jump up to the glass tunnel and go to the right and go through the door there.

Make your way up this room, then go through the door at the top. In the room with the small glass tunnel, go through the door on the right. Shoot the two air vents in the wall on the right and roll through the tunnel. Go to the right. You can go through the door there to reach a Save Room.

Outside of the Save Room, jump up to the ledge above, then go to the left. Make your way up and to the left, and when your path is blocked by a Powamp that puffs up on the right, shoot it with an Ice Missile from a distance to freeze it, then roll into a ball and jump over it. Go to the right and go through the door. In the next room, go through the door on the right.

Kill the Gravitts in this room, then go as far right as you can go. Run to the left while shooting the doors open. You will break through some Boost Blocks in the floor. Fall down through the hole where the Boost Blocks were, then go through the door on the right.

Kill the Gravitts on the floor and ceiling. In the right side of the room, there is a hole in the ceiling just before the door. Go to the far left of this room and run to the right, then crouch before the door and jump to do a Shinespark through the hole in the ceiling. You will break through some Boost Blocks up above. Go to the right before you fall back down, and take the Power Bomb tank. Before you leave this room, fall partway down the hole while pushing against the left wall to grab a hidden ledge on the left. Pull yourself up to enter a hidden tunnel. Go to the left to get a Missile Tank. Then roll back through the hidden tunnel and fall down the hole into the corridor below. Go through the door on the right.

Quickly Space Jump to the ladder at the top of this room to try to reach it before the Powamps appear. From the ladder, shoot a Missile at the ceiling, then jump up through the hole and roll to the left through the tunnel. Go through the door on the left.

Bomb the thin walls in this room to get rid of them, then go through the door on the left. Go down below. You can now try an alternate method to see the secret cutscene mentioned earlier. (If you are not interested, skip to the next paragraph.) This video demonstrates how to do it. Note that it might not work in all versions of the game. If you do this, then after you see the secret cutscene, go left through the Save and Recharge rooms, then go through the bottom left door, go through the small room, then go to the top right corner of this room and bomb the block. Go through where the block was, then go straight down. Run to the left while shooting to do a Speed Boost through some Boost Blocks in the bottom left of the room. Keep Speed Boosting to run through some more Boost Blocks. After you break through them, go to the upper left part of this room and go through the door there. Then shoot the floor and go down to the bottom of this room. Go through the red door at the bottom. Then go to the bottom left of the room, where there is a tunnel that leads back to Sector 5. Stand in the far left of the tunnel, then run to the right, and when you reach the top of the second ramp, jump to break through the Boost Blocks. From here, you can use the map to go to the far right side of Sector 4, and follow the path to return to the room with the three Powamps.

In the bottom right corner of this room, go through the red door on the right. This is the Data Room. Use the machine to get Diffusion Missile data. Now you can charge up your Missiles by holding R. When they hit something, they will freeze surrounding enemies. Exit the Data Room.

Before you go farther, shoot a charged Diffusion Missile to freeze the three Powamps. Roll to the left through any of the three tunnels, then go to the bottom left of the room and walk to the left through the metal walls. In the next room, use Missiles to destroy the purple barrier, and go to the left side of the room. Roll under the wires and bomb the wall to get a Missile Tank. Go to the right to return to the previous room.

Go to the upper left corner of the room and go through the door. Then go to the bottom left corner of this room and go through the door. In the small room, go through the door on the left. Drop a bomb against the left wall to open a hole, then roll into the tunnel and drop a bomb to fall through a hole. Go to the bottom of this area and roll to the bottom left corner. Use a Power Bomb there, then roll through the new tunnel to get a Power Bomb tank.

Now go to the Navigation Room. Adam says to return to Sector 6 to destroy the rogue Security Robot that you battled in PYR.