In the Navigation Room, Adam tells you that the ARC Data Room is secured by yellow Level 3 hatches. You must find the Security Room and release the lock to access the Data Room.
Go through the Save and Recharge Rooms, then climb down the ladder, and grab onto the ladder on the left. Kill the Zeela from the ladder, then climb to the top and aim right and shoot two Missiles at the wall to open a passage. Pull up into it and go through the door at the end.
There are Chute Leeches on the floor around here; be careful, they are hard to spot if you're moving quickly. When you approach them, they jump up and float down, and they will drop a substance that damages you. Drop to the bottom, head right, and follow the path to the door. Go through.
There are many Wavers in this room. Shoot them rapidly to kill them before they hit you. Follow the path, and when you are blocked, shoot the floor to continue on. Down below, exit through the left door. Kill the three Zeela, shoot open the door, then make a running start from the gate towards the right. In the previous room, you will Speed Boost through the floor. Continue along the straightforward path, bomb the little block in your way, and go through the door.
Bomb the wall to open the barriers in this room, releasing all the Wavers. Kill them as best you can, then exit right. Drop below. The first door you see is a dead end. Bomb the floor and drop below. The left door is a Save Room, so save, then continue left. Go through this room with two Kago just sitting there, and continue left until you reach the Security Room. Release the Level 3 hatches, then continue left.
Go up this shaft, trying to avoid the tons of Zeela. The square blocks are made of Pit Blocks, so don't stand on them. At the top of the ladder up above, shoot left to break open a block in the way, then hold L or press up-left to shoot diagonally at the other block. Jump onto the platform, and shoot above you to open a hole in the ceiling. Jump up, enter the Save Room, use it and exit right.
Open the gate, and exit right. Continue right to the big room. Jump up through the floor you bombed earlier, and go through the door at the right. Open the gate and continue to the Data Room, and download the Ice Missile data. Exit right and bomb the floor. You'll fall quite a ways down; try to avoid the Rippers on the way down. Climb to the top of the ladder, then shoot the Ripper at the top with an Ice Missile when it's centered in the room to freeze it. Jump on it and enter the room to the left.
This Energy Tank is another enemy in disguise, so approach it slowly then kill it with a Missile when it floats up. Bomb the left wall to reveal the real Energy Tank. Go back out to the shaft and fall to the bottom. Roll into a ball and go to the little niche to the right, jump up and press right to get into a passage. Go through, and shoot the ceiling at the far right to open it. Kill the Zeela but leave the X alone; let it re-form into a Chute Leech. Approach the Chute Leech to make it float up, then freeze it with an Ice Missile and use it to reach the ledge above. Kill the Zeela above but once again don't touch the X, which turns into a Ripper. Freeze the Ripper when it's about centered underneath the niche in the ceiling, then stand on it, shoot the ceiling, and grab the Missile Tank.
Go back below and roll through the tunnel to the last big shaft. Go through the yellow hatch. The Kago here will be transformed by an X; freeze it, stand on it, shoot the ceiling and pull up above. Exit through the door here. Find the Zeela in here and get a distance away from it and kill it, and don't touch the X. Kill the second Zeela that forms, leaving the X alone, and it will transform the Kago below. Go down and freeze it, then make a running start towards the left from the edge of the platform, shooting your beam to open the door and Speed Boost through the wall in the next room.
Head up to the yellow hatch and go through. Jump to the corridor above, head right and get on the ledge below the thin wall (which can only be destroyed with a Speed Boost), and shoot the wall below it to the right. In the small side area, jump up above to the ledge to the right, then shoot the wall to the left to break open a tunnel. Pull into it and roll through, to fall through a Pit Block at the end. Make your way to the top left door and go through.
A fast-moving enemy will be flying past in the background, but you can ignore that (unsettling though it may be). Unfortunately, you will have to fight it later. Make your way around the room. Continue up past the yellow hatch, then freeze the Chute Leech when it hits the peak of its jump. Jump onto it to reach the upper ledge, then freeze this Chute Leech to reach the door above. Go through. Get rid of this Chute Leech and grab the Missile Tank. Then exit back to the big room.
Drop back down to the yellow hatch and go through. Kill the Geruta with two Missiles, then as a ball, bomb the top right corner of the room to reveal a Missile Tank. You have to pull up to reach it. Once you have it, exit left.
Suddenly, another unsettling thing happens: the music gets urgent, the Sector is bathed in red light, an alarm sounds, and the computer announces an emergency in Sector 3. Head up to the Recharge, Save, and Navigation Rooms. Uplink in the Navigation Room and Adam will tell you that the Main Boiler's cooling unit is malfunctioning, and the entire station could be destroyed if the auto-destruct explosives are triggered. Most of the systems in PYR are down. This is undoubtedly the work of the SA-X. You have 6 minutes to shut off the Main Boiler.
Hurry up to the Main Deck, and down the Elevator to PYR.