After you regain your Ice Missiles, there is an emergency in sector 3.
Hurry to the Boiler Room
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.
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 pull your way left, watching the lava to avoid spouts. Kill the enemies along the way as you go. 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 them, and climb up them to the door; go through.
Jump across the platforms to the left, and this time kill the Nahime with three Missiles, and get the Nova on the ceiling out of the way. Get on the ladder and kill the Novas on the ground, then jump up onto the ledge where the Novas were. Head right and jump up to the next ledge, kill the Nahime, and jump up above, careful of the Novas and their falling flame. Don't step on the little bridge, as 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.
Get the Side-Hoppers out of the way if you have to, jump onto the platform above the door you came in through, and get to the top left where a Living Door is on the door. Kill it, get the red X, and go through the door. Continue left to the control unit, where you see a scientist causing the meltdown. You have no choice but to shoot him; but you will discover it is in fact a Core-X.
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)
Log into the control unit to reactivate the cooling unit, and breathe a sigh of relief; disaster averted.
Make your way back to the shaft with the many Fune, and head through the green hatch on the right. Get rid of any Owtches in the way, and bomb the bottom right wall to open it. Freeze the Nova above when it's below the gap in the ceiling (which you can't clear from the ledge, but you can if you stand on the frozen Nova). Go through the door above.
Drop below and jump on just the first platform above the lava, but don't kill the Nova on the other platforms, as they are all made of Pit Blocks. Freeze the Nova and use them to go step-by-step to the right. Pull into the tunnel to get an Energy Tank. Jump into the tunnel above, go to the end and you'll fall below where you can get the Missile Tank. Continue to the end and you will fall below.
Open the gate and go through, and return to the shaft with all the Fune/Nahime. Get to the top and exit left. Bomb the top block in the left wall, roll left, bomb the block above you, jump into the tunnel above, roll 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 to the left, and drop below to the door at the bottom. Go through.
Shoot the walls ahead and go up to the second door above on the left. Go through and use the rungs to get across the lava, avoiding Side-Hoppers and lava spouts. Beyond the door at the end is a Missile Tank; grab it, then bomb the left wall. Continue left, shooting the things in your way so you will be able to do a Shine Spark through the block in the ceiling at the far left. When you're ready, Shine Spark through it, then press right so you end up to the right. Shoot the wall just below the part that sticks out, go into the small area, then shoot the wall at the top-right. Jump down and bomb the floor one space from the right wall to make an elevator pop up. Step on it and jump up above, shooting the block in the ceiling. Jump up, then shoot left to reach the Energy Tank. For a quick way back to where you need to be, return to the lower floor and make a running start, then crouch before the edge and shoot the door open, then do a Shine Spark to the right to get through the long lava room.
Return to the Navigation Room at the beginning of Sector 3.
Uplink for your briefing: since the X mimicked a scientist, it appears the X can absorb the memories and knowledge of their prey. Adam posits that even though it would have destroyed all the X in the station and the SA-X, perhaps the X tried to destroy the station because Samus is considered an even greater threat to X elsewhere.
Adam sees bio-signs on the Habitation Deck, and Samus must check for survivors. Adam has restored power to the Main Elevator.