First and Final Visit
From Samus' ship, continue left in Crateria, until the room with Green Space Pirates. Here, the right door is red unless you unlocked it already. Go through, then through the hall, to reach a room with a small pool and gold statues of the main bosses: Kraid, Phantoon, Draygon, and Ridley. In each of the statues' eye is a glow. This light shoots up, and the glow goes away and the gold turns to gray, if you come here at any time after beating a boss. Since they all should have been defeated by now, you should see all of the lights fly up, after which the statues will fall and the floor under the water will open. Drop here to an elevator, then take it to the last area: Tourian.
Head down. The right door has a Save Station which you should use, then continue left. Make sure you are ready, because you will be fighting Metroids, which are no pushovers compared to the Mochtroids in Maridia.
Metroids in the Halls
Be careful when you enter, because a Metroid will immediately fly for you. To defeat Metroids, first freeze them. After that, use either 5 Missiles or 1 Super Missile. If they attach to you, they will drain your energy. If this happens, you can use around 3 Power Bombs to kill them, or you can try escaping from their grasp with normal bombs, though this can be hard. The best way to use bombs to escape is to morph, lay a bomb, roll away from the bomb and roll back toward it as it explodes. If you are still having trouble getting the Metroids off, you can always leave through the door you came in and reset the room! It's best to try Screw Attacking while moving through the following rooms, since hitting Metroids in this state will push them back, protecting you from their quick assault and giving time for you to freeze them. Metroids give a good number of pickups upon death, so don't be afraid to use what you have.
Also in the following halls are discs of energy called Rinkas, shot from flashing circles in the walls. Rinkas can be shot or Screw Attacked to be removed, or merely frozen. The circles can only fire one at a time, so you can freeze one to prevent the circle that fired it from firing more.
This first hall has four Metroids. You need to remove them all to unlock the left door.
Next up is a vertical shaft. Go left to the platform, then jump and shoot below to freeze it. Try to stick near the middle of the platforms so you can freeze the Metroids from below in rooms such as this, and they should get stuck trying to move up, at least long enough for you to hit them first. You can drop left to the next platform from the first. Two Metroids here. After them, continue right.
Another horizontal hall. First, you'll see a narrower section. Approach it slowly to kill the Metroid inside. Once it's gone, go ahead and continue, but be careful of the acid below. Two more Metroids are on the other side, so get rid of them to move on.
Another vertical area. On each ledge here, it should be easy enough to freeze the Metroids below. So, take them out and continue down. This is the last of the Metroids you have to fight.
To the Last Boss
After the last shaft, you'll end up in an area with sand. There are powerful Sidehoppers here. You can defeat them with Super Missiles, but it's best to just Screw Attack left, then through the door.
In the next room is a motionless Chozo made of sand. Attacking it or merely touching it will cause it to disintegrate. Continue left, but know that it locks after you enter, so this door is a point of no return.
More enemies in sand form. Like the Chozo, they are still and touching them will cause the sand to dissipate. Eventually when going left, a Sidehopper will slowly emerge. No matter what you do, you cannot damage it. Then, a big Metroid swoops in and drains the life out of the Sidehopper. Afterwards, the large Metroid latches onto you, and there is nothing you can do about this. It will drain your energy all the way to 1, then let go. This is actually a bigger form of the Metroid larva seen in the beginning. When it lets go of you, it'll follow you around a bit unless you attack, where it will then fly away. Shoot the material in front of the left door that looks like webbing to continue left.
In this vertical area shoot the webbing to continue down. The left door contains Missile and Energy Recharge Stations, which you will need after the encounter with the Metroid. After that, take the right red door.
An empty hall, except for an eye door at the end, indicating an upcoming boss. Continue right to a vertical room. The middle door on the left leads to a Save Station, but since you passed the point of no return, you may not want to use it unless you are okay with being stuck here every time you reload the save. Take the bottom red door to progress.
The room will shake as acid rises, but it stops after a while. Keep left, and you'll see thin red barriers, called Zebetites. You must remove these to continue left. To do so, use around 10 Missiles or 5 Super Missiles, but be fast because they start to regenerate if you stop attacking. In addtion to acid and Rinkas in this room, there are turrets shooting at you every so often. Shots from it are quicker than Rinkas, but can be destroyed as well, but not frozen. You can stand right next to the Zebetite and quickly fire Missiles to get rid of it efficiently, just make sure you dodge all the obstacles heading at you.
After the first Zebetite is another, but this column has two smaller ones with a metal tube in the middle. These two are still attached, so hitting the bottom or top one will do damage to both. You may want to stand near the bottom one and rapidfire. After, Spring Ball through. Next up is another fully formed Zebetite. Finally, after that is another pair of smaller ones. After this last Zebetite is the final boss: Mother Brain. If you want, you can return right to the Energy and Missile Recharge Stations. Any Zebetites destroyed will remain so should you exit and reenter.
If you are familiar with Metroid on the NES, the concept with the final boss is the same here. Mother Brain remains in a glass container, which you will need to shoot 6 times with Missiles to make an opening. After that, you can keep shooting the glass to make it easier to hit Mother Brain herself, or just aim at the boss' head. Even in this stationary form, touching the brain, glass, or even the platform will damage you so it's best to remain on the single small platform instead of trying to get on the one with Mother Brain. All the while, turrets will continue shooting, and Rinkas will fire as well, with acid below. It is suggested that you use Missiles first. After around 30 Missiles or 10 Super Missiles aimed at the head, the acid, turrets, and Rinkas will be destroyed. Also, the platforms will be gone, and the boss' head will drop. Unlike the NES game, this is not all that is required to end things. Mother Brain grows a body, and this leads to the second phase of the battle.
Final Battle: Phase Two
To do damage, aim at the head with Missiles, Super Missiles, or charged shots. The best strategy might be to remain near the right corner, aiming diagonally up. Start by constantly shooting Missiles until they're depleted, then Super Missiles, then charged shots. Mother Brain will try to walk toward you, giving you less space and pressuring you, but if you keep firing this will ensure that the boss remains back so you can jump and move when needed without worry. Alternatively, you can try to shoot directly under Mother Brain, which may give you some more room to dodge attacks, but it is still preferable to try and dodge the attacks from the right since this allows you to deal damage quicker, and you don't have to worry about Mother Brain stepping forward unexpectedly or any surprise attacks from below.
Initially, Mother Brain has three main attacks to watch out for. First, there is a laser shot horizontally from her eye, which is similar to the lasers shot by Space Pirates. So long as you aren't across from Mother Brain's eye when this is fired, you should be fine. Next, Mother Brain has a bomb attack. Unlike the multiple bombs of the Torizos, this is only a single bomb, yet it is still more devastating. It bounces around five times before exploding horizontally, covering most of the floor. Try to jump before the last bounce to avoid the blast. Also, you can't shoot it to destroy it. Next, she has an attack in which she fires a multitude of blue rings. It can be tricky to avoid, but watch for when she opens her mouth and roars. If the rings appear, immediately jump to avoid the attack, and be prepared to move or jump again for any follow-ups.
After taking a good amount of damage (16 Charged shots or 45 Super Missiles), Mother Brain will add a new attack to her arsenal. With this, she fires a stream of circular energy. You can predict this will happen because she will pull her arm close to her body. When you see this, be ready to dodge it. This beam is especially dangerous, but you can Screw Attack to avoid damage from it. If you want to play it safe, dodge this attack, fire a couple of times, then Screw Attack while anticipating the attack again. You can just repeat this for some time.
After 4 more Charged shots, Mother Brain will introduce one more attack. With this, she charges energy in her brain, then releases a cone of multicolored energy from her eye, dealing a large amount of damage and taking away any remaining Missiles, Super Missiles, and Power Bombs. There is no avoiding this attack. You must have at least 3 Energy Tanks full (or the equivalent with Reserve Tanks) to survive it, or you'll get an instant Game Over. If you survive, you'll be forced down, where you'll have to keep pressing directional buttons to recover.
Eventually, after your Energy Tanks are depleted and you are close to death, it'll be impossible to recover, and Samus will stagger uselessly should you try to get up. Mother Brain goes in for one more multicolored beam to finish you off, but suddenly the Metroid larva from earlier flies in and attaches to Mother Brain, draining her energy. The Metroid then latches to you, and restores your energy to full.
Now, Mother Brain will recover from the Metroid's assault and will desperately try to use her first three set of moves, faster than before. Once control is given back to you, you'll notice upon firing that you have a different beam. This is called the Hyper Beam, and replaces all beams including the default one and the Charge Beam. This means of course that it cannot be charged, but holding the button will allow you to rapidfire it. To deal with Mother Brain, use the same strategy as last time. Simply remain right, and rapidfire diagonally left at the head. The attacks might seem harder to avoid, but constantly firing will interrupt Mother Brain at times, giving you an advantage. After some time (around 36 Hyper Beam shots), the body will explode and the head will fall, meaning that victory is yours.
Once Mother Brain is defeated and the head is gone, a countdown will begin. You must return to your ship before the countdown ends in 3 minutes. The right path is blocked, so you must head left. The wall will explode, allowing you through.
In the next room, shoot the shutters in the path to remove them, then take the door down. Space Pirates will appear in the following rooms. In this next one, shoot or avoid the space pirates then take the bottom right door.
In this next room, you have a choice to go up or down. The bottom path is quicker, but you have to Shinespark. Speed Boost along the bottom floor, and duck to store it before hitting the right wall. Then, Shinespark to the door.
Otherwise, there is the longer way. With this path, go along the platform above the bottom floor with the Space Pirate. The path upwards will continue left, then jump at the first opening while moving left. Then go right, killing the Space Pirates, to the door.
In the next room, start by going up and right. Then, go left when the path ends right and down the thin shaft. Acid will start to rise should you delay. Head up after the shaft, to an opening in the upper left. Start running and holding the shot button here and continue this into the next room.
Tan Gray Space Pirates are waiting, but don't worry about them, as a single Hyper Beam shot will kill them both. If you were still holding run from the last room, you should be able to run through the wall at the end and charge a shinespark back in the vertical shaft with platforms in Crateria. If so, go the the far righthand wall and spark straight up and you will go through all the platforms bypassing the tedious jumping section from earlier in the game. If you miss the shinespark, don't worry, start jumping up the platforms. As if the timer is not enough of an incentive, acid will rise in this room to hurry you along. So, make sure to be both fast and careful in your climb. Take the top door back to the rocky and grassy part of Crateria. Continue up from there, and the outside portion with the ship is nearby. You can see an easter egg if you detour a bit, however.
Saving the Aliens
The majority of the doors are locked. One exception is the door to the area where you got the Bombs. So, while heading right at the top of the rocky area, you can morphball down the tunnel and head right. Inside the room where you got Bombs and fought Torizo, you will see the Etecoons and Dachora. The door will lock behind you. Shoot the right wall and the aliens will escape through the opening. You cannot go there yourself, but the door will unlock so you can go back left and back up.
To the End
Continue right to get outside. The ship is here, so jump atop it and stand in the middle. Press on the central part to get inside. If you were able to do this before the countdown ended, you will see the ship fly up, off the planet. The ending will then commence.
If you saved the aliens, watch the right side of the screen as Samus' ship flies forward. You will see a speck in the distance flying right, presumably the aliens escaping in a spaceship.
Eventually, you'll get a short scene involving Samus, which is different depending on the time it took you to complete the game. See the Secrets, Tricks and Glitches section for more information. You will then see your item collection rate, which should be 100% if you got everything outlined in the guide. The game will stay on this screen until you turn off the game or reset.