Uplink in the Navigation Room, where Adam will merely point out the location of the Data Room. Head through the Save and Recharge Rooms, then descend to the bottom of the shaft beyond. Exit through the yellow hatch to the left. Get rid of all the Zeela, and then jump up through the bottom of the square with the Missile Tank in it to get it (the invisible hole is on the left side).
Go back out and follow the relatively straightforward path to the Data Room (seeing that scary shadow pass in the background of the big room with glass walls). Download the Power Bomb data in the Data Room (you can only carry 10 to start with, so use them conservatively), then exit right and use a regular bomb on the floor below to fall down the long shaft. Exit left through the yellow hatch.
Save to the left if you want, and go through left door of the Save Room to find a red Zeela that will release a red X, replenishing a lot of energy (you'll need it in a moment). Back in the room to the right of the Save Room, drop a Power Bomb and a block in the floor will be destroyed. Fall through it and go through the door.
The SA-X follows! Quickly run to the left and jump onto the wall. Unfortunately, the SA-X will not leave if you just stand there. If you fall behind the other side of the wall, the SA-X won't see you. Morph into a ball down below and drop a Power Bomb, and as soon as it goes off (alerting the SA-X to your presence so it starts shooting at you), jump up to the top tunnel you revealed and roll through. Try to jump any beams the SA-X shoots your way as you hurry to the left and through the door to safety. The SA-X will not follow you into here.
Kill all the Zeela in here (including a red one for a red X, which you may sorely need after your encounter with the SA-X if you weren't careful), and drop a Power Bomb to destroy some blocks in this room, including some blocking a Power Bomb Tank, which ups your Power Bomb carrying capacity by just 2. Climb the ladder and jump off it to the ledge above. Don't exit through the undamaged door; instead, drop a Power Bomb to break a big hole in the ceiling and reveal a ladder. Climb up, then make your way to the top of the shaft by freezing the Rippers above you and using them as platforms. You'll want to freeze the third one when it's near the right side of the shaft. Exit through the door at the top.
Grab the Power Bomb tank, exit, fall down below to the undamaged door, and go through to the Security Room where you released the lock on the yellow hatches. Pass through it, and climb up to the second ledge in this shaft. A Power Bomb will reveal a ladder along the left wall; climb up it to the Save Room and save. Exit right, open the gate, and exit right again. This big, gross barrier can be destroyed with a Power Bomb, so set one off and exit right.
Go to the right and jump up above, then head left to where you see another ugly barrier. Use a Power Bomb to destroy it and open a narrow passage to where it was. As a ball, jump into it and go through, and exit through the door here.
There's a Power Bomb Tank to the left that's a bit tricky to get, because there are many hidden Pit Blocks in the narrow tunnel above leading to it. You must freeze the Rippers along the way strategically so you can bounce onto them and avoid falling down the blocks. You can lay Power Bombs along the path to reveal all of the Pit Blocks to make your life easier. They are all near where the Rippers are floating, and there are also some just before the Power Bomb tank. Once you've revealed them, jump up above and make your way to the Tank. The second set of Pit Blocks is the hardest to pass; be patient and you'll get it eventually. Once beyond the tunnel, stand up and jump over the last set of Pit Blocks to the Tank. Stand on the blocks to fall back down, and exit this room.
Now return to the Navigation Room at the beginning of this sector (in the glass-walled room with the scary shadow use the yellow hatch at the bottom left) and uplink. Adam has important information for you, and simply tells you to return to your ship.