After you defeat Ridley, go to a Navigation Room and Adam will order you to go to the Operations Deck.
After you go up the main elevator from the Sector elevator area, run to the right while shooting your beam. You will break through some Boost Blocks. Go through the upper right door, then go down to the bottom of this room and go through the door on the right. Go the Navigation Room (no need to use the Navigation computer). After the Navigation Room, go to the top of this room and Screw Attack through the living barrier at the top, then go through the door beyond it. Jump onto the ledge on the right, then roll into a ball and jump while pressing right. You will enter a tunnel. (There is a tunnel below this one that is a dead end.) Roll to the right and ball jump to go over the block in the way, then keep rolling to the right to fall to the bottom of the room. Roll to the left to get the final Power Bomb Tank. This is the final upgrade for reaching 100% completion.
After you get the Power Bomb Tank, roll to the left to fall through a Pit Block. In the room below, roll to the left and drop a bomb to break a hole above you. Jump up through the hole and exit this room.
Back in the tall room, go downward and go through the first door on the right, then in the small room, go through the door on the right to reach a Save Room. I recommend saving now.
Go to the right from the Save Room, then go up to the top of this room and go through the door on the right. Go through the Navigation Room without using the Navigation computer, then in the next room, go upward and go through the door on the right. Then go up the elevator. At the top, go through the door on the left.
Charge up your beam, and Space Jump to the red hatch at the top left corner of the room. As soon as you walk toward the Operations Room door, you hear a crash. SA-X has entered the room.
Charge up your beam if you haven't yet, then go down one ledge below the upper left door. Then wait there for the SA-X to land on the floating platform to the right, and shoot it with a charged shot as soon as it arrives. As soon as you hit the SA-X, start charging your beam again immediately, and go down to the far right of the room to wait for the SA-X to appear on the left.
The key to this battle is to never let the SA-X get too close to you. If you do, it will repeatedly Screw Attack you. Your job is to hit the SA-X with charged shots whenever it is not in a Screw Attack. After you hit the SA-X, it will Screw Attack toward you, and if you are far enough away when it does this, you will be able to get relatively far away from the SA-X without much difficulty, allowing you to shoot another charged shot as soon as the SA-X lands.
You can temporarily freeze the SA-X with Ice Missiles.
The SA-X will shoot Ice Beams at you if you give it enough time to do so. You can Screw Attack to avoid damage from these, but this may cause the SA-X to Screw Attack toward you at the same time.
After you hit the SA-X about 15 times, it will stop attacking and crouch in pain. Then it will transform into a huge monster. Fortunately, the monster is weak. All it does is jump up and down. Shoot charged shots at it, and run under it when it jumps toward you. After you shoot it three times with charged shots, it will transform into a Core-X.
You can Screw Attack this Core-X to make it drop X parasites if you need to recharge. This Core-X has an eye, so shoot a missile into the eye when it opens, and don't leave it alone for too long or it will shoot a beam from its eye.
After you defeat it, the Core-X will float away through the wall, so you will not be able to get it.
Now that the enemy is gone, Space Jump to the upper left of the room and go through the door there. Go to the left side of the room and use the computer. The computer will set the station on a collision course for SR388. This starts a 3 minute timer, so through the door on the right and go to the bottom right of the room, and go through the door there. Go down the elevator.
Main Deck Part 2
If you are not sure where to go, just pause to see the map and figure out your route. The 3 minute timer will pause as well. Go through the door to the left of the elevator, and in the next room go to the bottom left corner and go through the door to reach a Navigation Room (the computer is inactive). Go through the door on the left, go to the bottom left corner of the room and go through the door there to reach an inactive save room, then go through the door on the left, and in the small room go through the door on the left to reach a tall room. Go down to the bottom and go through the bottom right door. Keep going to the right to reach another tall room. Screw Attack down through the tall room, then at the bottom, go through the door on the right. The next room has gaps in the floor, but don't Space Jump through the room, because it is too slow. Just jump over the gaps and go to the right to reach the Docking Bays.
Go to the right to where your ship should be. You will see that it is not there. Run to the left, and an Omega Metroid will crash through the wall on the right. At this point, you can't harm it. You have to let it attack you. When it hits you with its claw, your energy will go down to 1.
After that, the Core-X from the Operations Deck floats into the room and transforms into an SA-X. Since Metroids are natural predators of the X, the SA-X starts attacking the Metroid with the Ice Beam, which damages the Metroid. However, the Metroid defeats the SA-X, and the SA-X turns back into a Core-X. Don't touch the Metroid or you will die. Collect the Core-X and your health and weapons will be refilled, you will gain the Ice Beam ability, and your Fusion Suit will take on the same colors as your original Power Suit. It is now time for the final battle.
If the Omega Metroid hits you with its claws, you will be knocked back, and will not be able to move for a few seconds, and you will be damaged quite a bit. Be very careful to avoid this. Hold the L button throughout the battle to aim upward, and make sure that you don't accidentally press down and start aiming at the floor.
Run close to the Metroid, shoot its body, and then quickly run away to avoid its claw attack. Repeat this until it dies.
Docking Bays Part 2
After the Omega Metroid is gone, your ship will fly into the docking bay. Stand under the middle of it and you will get in. CONGRATULATIONS! You beat the game!
Keep watching the ending scenes and press a button afterward to allow the game to autosave. The next time you play, your save slot will have a Metroid next to it, and when you load it, the map will show you your completion rate for collecting items, as well as the amount of time that you have played. The map will also show you if you have collected all of the items that can be found in the current area by showing you an upgrade symbol with a checkmark next to it. The Sectors will not be locked in this save file anymore, so you can collect anything that you might have missed in this save file before the final battle. You can also use this save file to start a new game that has the completion rate and completion time on the map from the beginning. These features make it easier to see the different game endings.
For an extra challenge, there is a way to create a New Game+ save file (i.e. a save file where you have beaten the game) that does not show the opening cut scenes at the beginning (the Japanese version lets you press start to skip the cut scenes in a New Game+, but other versions make you watch them each time). To do this, start a new game in an empty save slot, and beat the game without ever saving the game. When the game autosaves at the end, the save file that it creates will start the game in Samus's ship after landing in the station, skipping all the opening cut scenes, and the map will have the completion rates and completion time from the beginning.