After you regain your Ice Missiles, there is an emergency in sector 3.
Hurry to the Boiler Room
After you arrive in Sector 3, make a running start through the Navigation, Save, and Recharge Rooms (no need to uplink for a briefing this time), and you should Speed Boost all the way down to the hatch at the lower right. If not, drop down below and shoot the wall with the little tunnel to quickly get through. Drop down further, head left and fall below where you bombed the floor. Head right while shooting your beam to get through the walls to the next room.
After going through the bottom right door of the first room, jump up and use your Missiles on the Fune to kill it. Go all the way right and drop below, beyond the gate. Open it, then stand by the left door and make a running start towards the right to break the blocks in the floor in the next room. Walk left to fall through a Pit Block. Go through the door.
Drop to the bottom of this long shaft with all the Fune. Go through the left-hand green hatch below. Grab onto the rungs above and go left, watching the lava to avoid spouts. Kill the enemies along the way as you go. Be aware that the Varia Suit does not protect you from the lava, and you will move slowly if you fall into it. At the far left, go through the door.
Stand by the edge of the platform to make the Nahime open its eyes and spew fire. Jump the flame and wait for the Nahime to stick its head further out. Quickly freeze it, stand on it, and jump onto the ledge above. Go through the door. Be careful of the fire raining down from the Novas, and exit right. Make the Nahime come out, freeze it, then freeze the upper Nahime and jump on it to reach the door. Go through.
Jump across the platforms to the left, and when you reach the Nahime, shoot it with three Missiles to kill it. Kill the Nova on the ceiling, then get on the ladder and kill the Novas on the ground, then jump up onto the ledge where the Novas were. Go to the right and jump up to the next ledge, kill the Nahime, and jump up above, avoiding the Novas and their falling flames. Don't step on the little bridge, because it is made of Pit Blocks. Jump over it. Kill the Nahime ahead, then fall below to the door and go through.
The small platform ahead is made of Pit Blocks and will crumble, causing you to fall into the lava below, so freeze the Nova on it and jump on it across the gap to the door. Go through to the Main Boiler Room.
Kill or avoid the Side-Hoppers, jump onto the platform above the door, and jump up onto the platform above that. Go to the left and you will find a Living Door. Kill it, get the red X that it drops, and go through the door. Go to the left to find the control unit, where you see a scientist causing the meltdown. You have no choice but to shoot him. You discover that it is a Core-X that had transformed into a human.
This is a Core-X with an eye, so wait for the eye to open, shoot it with a Missile and jump to avoid the beam shot out. Remember, if you wait too long to shoot it, it will shoot a beam. Once it's defeated, grab the Core-X to recover your Wide Beam ability.
Sector 3 (PYR)
After you get the Wide Beam, stand at the console to reactivate the cooling unit. Disaster averted.
Make your way back to the tall shaft that has two green hatches at the bottom. Go through the green hatch on the right. In the room with the Owtches slithering on the center platform, go to the bottom right corner of the room and bomb the wall. Go to the right and freeze the Nova when it is under the gap in the ceiling, then jump on the Nova to reach the upper area. Go through the door there.
Go down to the lower area, then go to the right and jump onto the first platform on the right. The subsequent platforms are all made of Pit Blocks, so use your missiles to freeze the Nova and jum pon them to make your way over the platforms to the right. At the last platform, jump up to grab the ledge up above and roll to the Energy Tank. After you collect it, jump up into the upper tunnel and roll to the left to get a Missile Tank. Then keep rolling to the left to fall through a Pit Block into the lower area.
Go to the left side of the room, open the gate and go through, and go back to the tall shaft with the two green hatches at the bottom. Go to the top of the shaft and go through the door on the left. Bomb the middle block in the left wall, roll to the left, bomb the block above you, jump into the tunnel above, roll to the right, bomb the block in the way, jump into the higher tunner and roll to the end, bomb the block and jump up into the corridor. Destroy the purple barrier with three Missiles, go through the door on the left, and go down to the bottom of this area. Go through the door on the left.
Go to the bottom left corner of this area, then go up to the door that is above the bottom left door. Go through and use the rungs to go across the lava, avoiding Side-Hoppers and lava spouts. Go through the door at the end to get a Missile Tank, then bomb the left wall. After you have opened a hole in the left wall, run to the left and shoot your beam to break through the obstacles in your way. Just before you reach the far left wall (when you see some sagging metal in the background), crouch, then jump straight up do Shinespark through the blocks in the ceiling on the far left. When you start to fall, move to the right as you fall so you will land in the area above. Go to the right wall, jump up and shoot toward the hole beyond the wall. Go into the hole, then jump up and shoot the upper right part of the right wall. Go to the right and bomb the floor one space away from the right wall to make an elevator come up. Jump onto it, then jump to the upper area. Go to the left and shoot the block in the ceiling, then jump up and shoot to the left to reach the Energy Tank. Go to the left and fall down to the area below, then make a running start to the right, and before you fall off the short ledge, crouch and shoot open the door, then jump and press right to do a Shinespark to the right. You will quickly go through the lava room.
Return to the Navigation Room at the beginning of Sector 3. Adam will tell you that the Main Elevator is operational again. You are to return to the Main Deck and check for survivors in the Habitation Deck.
Go to the left and go up the elevator, and this time go to the center of the elevator area and go up the main elevator.