The game begins with a recount of the ending of Super Metroid. Almost defeated by Mother Brain, Samus Aran's life flashes before her eyes. However, she wakes, wondering what has kept her alive. The baby Metroid, the last of its species, has sacrificed itself to restore Samus' energy, and releases her, somehow equipped with the Hyper Beam, just before Mother Brain destroys it. Samus uses the new Beam to finally defeat Mother Brain, resulting in an explosion that eradicates Planet Zebes and all that remained on it, including the remains of Mother Brain and Samus' nemesis, Ridley. Samus escapes Zebes just in time.
Some time later, Samus awakens in a laboratory to the voices of quarantine officers. An officer asks her to move to the room next door, where she is given the restored Power Suit.
A quick warm-up[edit]
In this room, you'll perform some basic training exercises. To begin with, a Charge Beam. Face the blue target that appears, and press and hold 
to begin charging. Once the meter in the top right of the screen is full, release to fire. Do this to all targets that appear. Next up is the Morph Ball. Press 
to switch to Morph Ball mode. You can roll with 
, and press to drop bombs. Roll around for a while and try them out. To return to normal, press . The quarantine officer will now ask you to stand in the middle of the room. Once there, the floor will disappear from underneath. You'll need to Kick Climb out. To do so, press 
to jump, while pressing towards the wall. Once up, some enemies will enter the room. Defeat these by using the Charge Beam and normal Beam (press ). With all defeated, it's time to test your reactions. Some beams will be shot at you. Dodge these by pressing at the right moment to jump out of the way, a technique known as the Sensemove. If you do this with perfect timing while holding , the Charge Beam will be instantly charged. With those out of the way, prepare to get to grips with the Missiles.
To reload your Missile supply, hold 
vertically, and press and hold until your stock is replenished. This technique is known as Concentration, and can also be used to restore energy at dangerously low levels. Now, you can use Search View to look around in first-person view. Point at the screen, and hold 
to look around. If you look around the ceiling, you'll eventually notice an enemy lurking in the corner. Point at it and hold to lock on, and press to launch a Missile. It will fall down and attack. Use all your techniques to defeat it, including another new one, Overblast. To perform this, charge a Beam with , then jump on its head with , and release for a headshot. Note that eventually, this holographic creature will eventually become missile-resistant. Once it's defeated, the quarantine officer will lower shields over the windows. He'll ask you to switch to Morph Ball form, and drop a Power Bomb. To do so, hold while in Morph Ball form until the meter is charged (similar to the Charge Beam), and release to drop a small bomb with devastating power. This ends your warm-up session.
Codename: Baby's Cry[edit]
With the warm-up completed, Samus is called to the Meeting Room to confirm completion of her previous mission; the destruction of Zebes, and extermination of the Metroids. With this done, Samus leaves in her ship. Time passes, but eventually she receives a signal from a remote region of space, codenamed "Baby's Cry". Without hesitation, Samus alters her course to the source of the distress signal, the Bottle Ship facility.
Upon arrival, it appears that you are not the only person to have picked up the "Baby's Cry". Point at the other ship in the area; specifically the logo branded on its nose. This, it seems, belongs to the Galactic Federation. Follow the path through the door to the right. At the end, Samus narrowly avoids gunfire, which is halted by one of the group of soldiers, Anthony Higgs, a member of the Galactic Federation Army. Also among this group is Adam Malkovich, the platoon's Commanding Officer, and also Samus' former Commanding Officer, during her time as part of the Galactic Federation. She explains the circumstances that led her there, but Adam refuses to explain his platoon's mission, on the grounds that Samus is now an outsider.
Meanwhile, some other soldiers have been rigging up a bomb to a sealed door, which does not work. Point at the partially-destroyed door, and shoot a missile at it. This breaks the seal, allowing entry. The Galactic Federation soldiers venture further into the Bottle Ship. You should follow. However, Adam has not authorised the use of bombs or missiles; you can't use them again until he allows you to. Enter the door and follow the path through the next room. In the next area, you'll be jumped by a fly-like enemy, who knocks you down to a lower level. Defeat every enemy you find down here. These are weak; one simple Beam shot each will take care of them. To the right of this area, you'll notice a green target on the outer wall of a wire-frame cage. Lock on to it (point at it and hold ) and shoot it with a Charge Beam. It will rise enough for you to be able to slip under in Morph Ball form. Once under, return to normal and climb up, by jumping up each platform. Continue going up; there is a door at the very top, past several enemies. Run through the next room, being wary of anything dropping from the ceiling. When you enter the next room, some enemies will enter from a door to the right. Defeat these and move on up the staircase. At the top, stand near the red terminal to unlock the door. Enter. The next room is simple; Kick Climb up the broken elevator shaft and exit. Once you enter the next room, the door will lock behind you. Defeat any enemies and pass straight through. Cross the bridge, knocking off any enemies you meet. In the next room, the elevator is powered off, meaning you'll need to jump up the ledges to the top instead. At the top, go left to the open door. This room is a Navigation Booth. Many of these rooms can be found throughout the Bottle Ship; they allow you to save your game, and restore all energy and missiles by standing on the platform. Do so to unlock the next door.
Boss: Brug Mass[edit]
Head straight up the corridor to meet the Galactic Federation 07th Platoon again. The soldiers are gathered around the corpse of a researcher. A bug emerges from underneath the corpse, and approaches one of the soldiers, Lyle Smithsonian. Lyle kicks it away and destroys it. Soon after, thousands more emerge from the walls, and form the game's first boss, the Brug Mass. Avoid its attacks, and switch to Search View at the safest opportunity. However, your Charge Beam is not enough. All you can do is avoid its attacks. None of either your or the soldiers' current arsenal is capable of taking down the Brug Mass, so Adam authorises freeze guns for his soldiers, and your Missiles. Further avoid its attacks, then point and lock on to its eye, and shoot a missile at it. This will cause it to slam down on the ground, and its tentacle will become trapped. Wait for the soldiers to freeze the tentacle, then launch a missile at it to destroy it. Rinse and repeat for the other tentacle. With both destroyed, the Brug Mass will start jumping around the area. Avoid it, and use the same attack method as before. With its body destroyed, the eye-like beetle will attempt to escape. One missile will kill it. After this, Adam will ask that you assist his platoon in their mission, but also that you follow his commands.
System Management Room[edit]
After a cut-scene, he will assign each soldier to a different area of the Bottle Ship. You are to travel to the System Management Room, to restore power to the Main Sector. Adam authorises the use of Morph Ball bombs, but not Power Bombs. A map will appear displaying your destination. Exit the room. If you defeat all enemies in a room, blue dots symbolising item locations will appear on the on-screen map. You may notice a small hole along the right of the corridor. Change to Morph Ball mode, and travel down it. Destroy the barrier with a bomb, and continue down for a Missile Tank, which increases your maximum missile capacity by one. Leave this room to the south, and stop at the Navigation Booth before continuing. In this elevator room, drop down to the bottom and exit. Head don the staircase to the next room. The door to the System Management Room is locked.
Instead of this, head south a little to a broken wire-frame pipe. Switch to Morph Ball form, and roll up it. Break open the gate at the top with a bomb, and continue on for your first Energy Tank, which increases your maximum energy capacity by 99 points. Roll further on to another gate, and destroy it too. You'll drop into the System Management Room. Walk up to the terminal, and activate it. However, two large nests are blocking the current. Destroy all enemies that come from these nests, then destroy the nests themselves. Three missiles each should be enough. With those gone, re-activate the terminal to restore electricity. Exit through the newly-opened door, and backtrack to the room highlighted by the map, where Adam awaits. As you begin to cross the bridge in the previous room, however, it will withdraw, causing you to fall to the ground below.
Three enemies await, each of which need an Overblast. Once they're dealt with, head north to an area perfect for Kick Climbing. But it isn't, yet. Look to the top, and you'll notice a missile target. Lock on and fire at it, then Kick Climb up. In the Elevator room, the elevator now works, so take it to reach the top level safely. Head to the Navigation Booth and save, then run through the corridor back to Adam. Your next destination is Sector 1, where Lyle was dispatched to. Adam will open the door to the right, which leads to the Main Elevator Room, and Sector 1.