The SC will be quite surprised that you've recovered the Plasma Beam, but it'll recommend against taking on the SA-X (darn). The SC will then inform you that an explosion has occurred in the Sector 5 Data Room (I feel so bad for these Data Rooms), and that you need to investigate immediately. Leave this sector for now and head back over to Sector 5. Once in the Navigation Room there the SC will tell you about the cause of all the damage here.
Remember seeing that huge shadow flying around the background of the massive room with blue Chute Leeches? Well, it's broken out and is on a rampage. This creature, known as Nightmare, was built for military applications, so it has some heavy offensive weaponry. We'll have to track this Nightmare down and destroy it as a Core X has most likely infested it and taken control. Go right past the Recharge Room and drop down the next shaft. Go into the massive room where you saw the Nightmare's shadow flying around to find it in a complete mess.
If you scale the room up to the door on the top left corner you'll be able to pick up Missile S5.03 & Power Bomb S5.04 from here. Once you've grabbed both items, head down through the wrecked door in the bottom right corner of the giant room. You'll now be back in the giant frozen room, but it won't be frozen anymore. Down below the ice has completely melted and filled the room with water, but straight across on the right side of the room you'll notice that the red door is gone, so you can proceed through. Through the ceiling in the next room you'll be able to reach Power Bomb S5.05.
Continue on to find yourself in a room above the Data Room with a hole in the ground. If you drop down below you'll find the sorry remains of the download station, keep going through the opening up on the right. Proceed down the following wrecked corridor while watching out for various enemies, the next room contains a large shaft leading down. Shoot out the blocks in the floor ahead and drop down into the water below.
You won't be able to come back through this way so we need to find another way out once Nightmare's dealt with. Watch out for the Skultera and Zebesians in these underwater rooms, they'll often try to combine to produce a swimming Zebesian.
Go through the door at the base of the shaft and proceed down the submerged corridor. You'll have trouble moving around underwater but it'll only be for a little while longer. Go over to the right side of the corridor and climb up the platforms above. Go through the door up ahead and climb up the following shaft (watch out for the swimming Zebesian). Up through the next door you'll find yourself in a large waterless room.
Fry the creatures up on the roof ahead and shoot open the ceiling. Climb and go through the open door on the left to find Power Bomb S5.06 hidden in a small room. Grab the item and go back into the large room. Go right and jump up through the hole in the ceiling, through the right door you'll find a Save Room, lay a Power Bomb in front of the door to reveal hidden tunnels on the left wall.
Crawl through to find a door leading to a Recharge Room, here you can also find Power Bomb S5.07. With the item in hand go down through the wrecked door below the door leading to the Save Room. Watch out for the multitude of creatures in the following corridor, then climb up through the opening in the roof. Fry the Eyeball door up here and go inside. In the next room you'll spot Energy Tank S5.02 straight ahead, lay a Power Bomb to reveal a tunnel leading to it.
Once you've grabbed the item roll over to the crumbling blocks in the floor and drop through to finally face Nightmare in a large room. Refer back to the bosses guide for tips on beating this strange looking monster.
Upon defeating this weirdo you'll finally recover the awesome Gravity Suit! Now you'll be able to move around freely in underwater environments, and the lava lakes in Sector 3 won't harm you anymore. Neat. We can't get back to the Navigation Room by the way we came in here, so we need to find another way out. Walk over to the right side of Nightmare's room and run through the door on the left. Keep running to Speed Boost through the wall in the next room to get through. From here go back down to the underwater corridor with all the Zebesians and Skulteras.
Once there, go back into the shaft on the left side to find Energy Tank S5.03 hidden above. Once you've found it go back into the long underwater corridor and clear out all the enemies. Open up the door on the right end of the corridor and dash back to the left side. Run over through the right door to activate the Speed Booster, then once you break through the two walls in the following corridor quickly duck and Shinespark up through the ceiling between the two walls to find Power Bomb S5.08. Now that we've cleared this area of items it's time to head on. Drop back down into the corridor by way of the crumbling blocks ahead and run over to the right.
Keep running to activate the Speed Booster, in the next room you'll find yourself back in Sector 4. Keep running up the ramp and duck when you reach the flat section between the two ramps. Aim up to the right with L and Shinespark over to break through the solid wall up ahead. It's best to Shinespark from here so that you avoid all the annoying enemies that get in the way further up. The other door leading out of this room on the left side is red so we can't get through that way. Go through the right door to reach an area simulating a deep sea environment, even the music fits in perfectly with the atmosphere. Save your game in the room opposite before heading on.