After the restricted lab is jettisoned from the station, you will see an automatic scene in the next Navigation Room that you go to. After that, you must return to the Main Deck.
Go to the Main Deck
Exit right and go up the elevator to Sector 1. Space Jump around this room and exit through the top right door. Screw Attack through this corridor to kill the Amoebas, and exit right to a shaft. Space Jump up and roll through the tunnel to the door above on the right. Shoot open the gate in the small room and exit right to a shaft, and Screw Attack through to the bottom. In the next room Screw Attack through, trying not to land in the green stuff. Screw Attack a hole behind the gate and shoot it open, and exit. Screw Attack up the shaft, then exit left twice, and exit through the top left door here, go through a small room, and head to the top of this tall shaft. Exit left, get in the lava, and use the green hatch at the bottom left. Screw Attack up the shaft to the blue hatch and go through, then exit through the top left door in the first room of the Sector to reach the Recharge, Save, and Navigation Rooms leading to the elevator up. Go up to the Main Deck and take the Main Elevator up.
Start running to the right while shooting and you'll break through some Boost Blocks in the third room. Take the door across from where the blocks were and head down the shaft and through the Navigation Room at the bottom right. The very last upgrade of the game is through the green hatch at the top right of this shaft, beyond an X-Barrier that can be destroyed by a Power Bomb. Destroy it, go into the room, and get on the ledge and morph into a ball. Ball Jump and then hold right at the very top of the room to get into a tunnel (there's a tunnel below that is a dead end). Ball Jump to the right over the block in the way, then once you land below, roll left to grab the final Power Bomb Tank and fall through a Pit Block. Roll to the left and drop a bomb to break a hole above you. Jump out of it and exit this room. That's it, 100%.
Back in the shaft, use the hatch just below the one you came out of to reach a small room on the way to a Save Room. This is the Save Room of no return, so save now, then exit right.
Use the hatch at the top of this room to go through a Navigation Room. Then use the door above to reach the elevator to the Operations Deck.
Exit left from the elevator. Charge up your beam, and Space Jump to the red hatch at the top left corner of the room. As soon as you walk towards the Operations Room door, you hear a crash and the music gets urgent, indicating that an SA-X has entered the room. Quickly drop to the bottom floor.
One of the last battles of the game, it can be pretty tricky, but if you fall into the right pattern, you'll survive.
The SA-X is vulnerable to charged shots, and you can freeze it with an Ice Missile. You can also Screw Attack it, but if it's Screw Attacking too, you both get hurt and end up very close to one another, so this should be avoided.
The pattern to fall into is to stand a distance away from the SA-X, and jump any Ice Beams it shoots at you. If you do a Screw Attack, the Ice Beam will pass through you, leaving you undamaged. Don't rely on that to keep you safe, though.
After jumping over an Ice Beam, shoot the SA-X with a charged shot, then press the button again to start charging up once more. The SA-X will then jump towards you with a Screw Attack, which is when you should run under it in the opposite direction.
Get a good distance away, not too far, not too near, and turn around and try to get in a charged shot before it can shoot you with an Ice Beam.
Done right, you can simply jump the Ice Beam, shoot the charged shot, run under the Screw Attacking SA-X, turn around, and repeat. There may be times when the SA-X does a Screw Attack low to the ground, meaning that if you try to run that way, you get hurt. I think this will happen if you're too close to the SA-X, so keep your distance.
Once you hit the SA-X about 15 times, it will stop attacking and crouch on the ground, seemingly defeated. But then, it will suddenly let out a Samus-sounding scream and transform into a huge beast. Luckily, it's really weak, so if you're worn down from the battle with the SA-X, you shouldn't be in too much trouble if you're careful.
Shoot charged shots at the monster. It will jump high into the air towards you, so run the other way and it lands on your other side. Three charged shots should do it in, and it will transform into a Core-X.
This is one of those Core-X's whose vulnerable spot is an eye that occasionally opens, meaning that when you shoot the eye with a Missile, it shoots a beam at you, so take caution. If you Screw Attack it, it will release some free-floating Xs, so you can recover some health if you're in bad shape. Once it's defeated, it floats towards the ceiling, but then it floats away to the right through the wall and you can't get it... yet.
Space Jump up to the door you approached in the beginning, at the upper left, to the Operations Room.
Walk to the left and stand on the pod to tell the computer to change the station's orbit to set it on a collision course to SR388. Once you do this, a 3 minute timer begins, so quickly run to the right to exit this room. In the room where you fought the SA-X, exit via the bottom right door to get to the elevator. Take it down to the Main Deck.
Main Deck Part 2
If you're not sure where to go, just pause to see the map and figure out your route. The 3 minute timer will pause as well. You need to keep going left until you get to an (inactive) Save Room, then continue left to a shaft leading down. Go down it and exit through the bottom right door. Keep going to get to the Docking Bays.
To get down below quickly, Screw Attack the platforms to cut a swath through them to the door below. Go through. This corridor has gaps in the floor so you'll have to jump to get through. Don't bother Space Jumping through, it's too slow. Just jump the gaps to exit to the right.
Continue right to where your ship *should* be, only to find the outer membrane of a Metroid. Try to exit left, and next thing you know an Omega Metroid crashes through the right wall. It's invulnerable to all your attacks at this point, so just let it beat you up until your energy is down to 1. You'll end up on the left side of the room.
Just when it looks like you're going to kick the bucket, the Core-X that floated away in the Operations Deck appears, and transforms into an SA-X. It looks like you're in even more danger, but the SA-X doesn't attack you; instead it uses its Ice Beam on the Omega Metroid, which damages it. Not good enough, unfortunately, because the monster swipes at the SA-X with its claws, knocking it to the floor. The SA-X transforms back into the Core-X. DO NOT TOUCH the Omega Metroid, or you will die. Jump up to touch the Core-X, which fills your energy tanks to maximum, gives you the Ice Beam ability, and changes your Power Suit to look as it did before it had to be surgically removed (but it is still the Fusion Suit; just in the colors of your old Power Suit).
This is it, the final battle!
If the Omega Metroid slashes you with its claws, you'll get knocked back and won't be able to move for a few seconds, and you'll also be damaged considerably. Avoid this at all costs. You'll want to hold the L button for this entire battle so you're shooting at an angle upwards. Be careful not to press down accidentally or you'll be shooting at the floor.
What you want to do is run close to the Omega Metroid and quickly shoot its body a couple of times (at an angle is best), then QUICKLY run to the left so you're out of its reach when it slashes the air. Sometimes the Omega Metroid will jump backwards, which means you can shoot it a ton of times as it retreats. Just be careful to run away if it stops. Once you hit it enough times, it will explode and be dead and gone for good.
Docking Bays Part 2
Watch as your ship comes into the bay, stand below it and you'll get in. You did it! You b eat the game, and now you can watch the ending scenes with the satisfaction of a job well done. Enjoy! Remember not to turn off the game during the ending, because once it's finished, the game will make a record that you beat it, and you'll have a couple of new options in that save slot. Look at the endings list for a description of each ending and the requirements for getting each one.
The save slot in which you beat the game will now give you two new options whenever you choose "start". You can either start over or continue. If you want you can continue from the very last save point before the final battles, if you didn't collect all the upgrades before Adam locked all the Sectors and want to go for 100% now. If you choose "start over", you start a new game. If you save the game once you start over, it will overwrite the saved game you had just before the final battles.
However, the important feature of the save slot where you won the game is that whenever you pause and look at the map, you see some new statistics. On the bottom left will be the game clock, telling you how long you've been playing. This can be useful for trying to get one of the five different game endings. Also, in the top left you see the total of Energy Tanks, Missile Tanks, and Power Bomb tanks in the current sector, as well as how many you've collected in that sector so far.