After a close shave with SA-X in TRO, Samus must investigate SA-X's activity in AQA.

Sector 4 (AQA)

Uplink in the Navigation Room. Adam tells you that AQA is home to a high-speed creature called Serris. You have been authorized to kill it so it can't get into other sectors. Adam warns you of electrified water in some areas.

Go left to go through the Save and Recharge rooms. In the large room, go to the left to reach a door at the lower left of the room. Go through, then go through the door on the left in the small room.

Jump onto the ledge above and to the right, killing the Scizor above you, and jump to the upper ledge. Drop a bomb at the block at the top left, kill the Scizor on the rungs, and grab the rungs. Go to the far left. Drop below onto a block (the chains show you where it is). Jump from block to block to reach the door at the top left, and go through.

Be careful of all the Scizor along the walls and Skultera in the tanks. Jump up onto the upper-left ledge, go down into the tank of water, and go through the door. Kill the Skultera-X, use the ladder, then press right at the top to jump over to the ledge. You can go through the door on the left to reach a Save Room. After you leave the Save Room, go to the right. After you go past the Scizors, jump up to grab the small ladder, then jump onto the other ladder. Shoot upward to kill the Scizor on the ceiling, then jump into the tunnel up above. Go through the tunnel, then go through the door on the left. Take the Energy Tank.

Go back the way you came until you reach the room with multiple small water tanks. Use the ladder to climb out of the tank, then go to the bottom left part of the room. Go through the door there.

The water in this room is electrified. Shoot the big block above the door, then roll in the tunnel and drop a bomb next to the long block that is blocking the rungs above. Grab onto the rungs and go to the left. Jump up through the gap in the ceiling to reach a new room.

Go to the left side of the room and climb up the ladder. Keep climbing it until you roll into a ball in a secret tunnel. Roll to the left to reach a new room. Kill or avoid the Owtches and take the Missile Tank. Roll back through the tunnel return to the last room.

There is nothing else you can do here, so just drop below and through the gap in the floor to the last room. Bomb the wall to the left, then go through the door on the left. Don't go through the blue hatch yet. Instead, shoot the block above the door on the right. Climb up the ladder, then grab the rungs in the ceiling and go to the left side. On the ledge to the left, shoot the ceiling to break it open, jump to the area above, then roll through the tunnel on the right and bomb the blue block. Climb up the ladder, then grab the rungs in the ceiling (the floor below the rungs is made of pit blocks), then on the next ledge, shoot below you to break open the floor and fall below. Climb the ladder, shoot the blocks above you to open the way, then jump to the right from the ladder and go through the door to find a Save Room.

You will soon face a boss, so you may wish to save your game here. Afterward, shoot the cracked block in the right wall and roll through the tunnel, then bomb the narrow block to open the path to the door. Go through that door.

You have reached the breeding tank, and you see Serris's remains. Go through the door to the right. Make your way up the ladders, then drop down to the Living Door. Jump quickly to avoid the yellow membrane since you are slowed down by the water. Once the eye is destroyed, take the red X that it drops, and go through the door.

Jump up onto the platform above the water and go to the right, standing on the non-cracked blocks. The cracked ones will crumble, and Serris will appear.

Serris

Serris's head is its vulnerable point, and can only be hurt with Missiles or the Charge Beam. Stand on one of the two middle platforms so you can jump and grab the ceiling rungs if needed. You can stand on the platforms and attempt to shoot Serris as it winds around at a high speed, but it will be difficult to see Serris in time to shoot it or jump out of the way. Alternatively, you can stay in the water and watch the ground for a cloud of dirt to appear, indicating that Serris's head is about to pop out there. However, since you move more slowly in the water, you may find it easier to stay on the platforms. Whenever you hit Serris, it glows and becomes invulnerable for a while and winds around even faster than before. Luckily, Serris only takes a few hits before it becomes a Core-X. Kill it as usual, then absorb the Core-X to regain your Speed Booster ability.

With the Speed Booster ability, if you run for a few moments, you will start to run at a high speed. You can use Speed Boost to break Boost Blocks, which are marked with a yellow arrow. When you are running at top speed, you can also jump while still charged up with a speed boost, allowing you to break Boost Blocks while jumping. Also, when you are running at top speed, you can crouch to store energy, then jump while stationary to perform a Shinespark. You can perform diagonal and sideways Shinesparks by moving in the appropriate direction immediately after you press the jump button. The Shinespark will also break Boost Blocks.

Sector 4 (AQA) Again

After you kill Serris and the Core-X, go to the upper right of the room and go through the hatch there. Jump onto the upper right platform and go to the right side of the room. (If you ran to the right without interruption, you will charge up a speed boost.) At the far right side, go down to the lower level and drop a bomb next to the wall on the left. When it opens up, go to the left side of this lower area, killing Owtches as you go. Then stand at the far left of this lower area and run to the right. Your speed boost will break the two Boost Blocks in the floor. Fall down through the hole where the Boost Blocks were, but press left or right so you won't fall straight down in the next room. If you do fall straight down, you will have to Wall Jump (spin jump against a wall, then press jump while pressing the direction away from the wall) to get back to this upper area.

In this area (marked with an open circle on the map), jump as a ball to bomb the long thin block to the left. Roll through the tunnel, then bomb the thin block that is against the walls. This will expose the ladder. Roll into the small niche in the corner of this area and drop a bomb to reveal a Missile Tank. After you take it, climb the ladder on the right, center yourself on it, and shoot two missiles to the left, between the two dots in the left wall. Roll through the tunnel that you opened, then go downward until you can go to the right. Keep going to the right, jump over a gap, and when you are standing on a small ledge on the right, jump up and shoot a hole in the wall. Go through that hole to get a Missile Tank.

Go to the left until you can go downward. At the bottom, you will fall through some pit blocks. You can go to the right to reach a Save Room. Then go left until you can fall down a hole in the floor. Go down that hole.

Go to the left, then go through the door there. In the room with the Scizor, and tanks with Skultera, use the bottom left door. Shoot the block in the ceiling, then roll into the tunnel to the left and drop a bomb next to the narrow block on the ceiling. Grab the ceiling rungs and go to the left side of the room. Go through the door on the left. Then go through the blue hatch on the left to reach the Pump Control Room. From the entrance to the Control Room, run to the left until you Speed Boost through some blocks. This allows you to reach the console. Stand in front of the console to lower the water level.

As the water goes down, climb partway down the ladder, then jump right to reach a Missile Tank. Roll into a ball and go through the tunnel on the right. Keep going to the right until you fall to the floor. Go to the right and jump up the platforms, then shoot upward to break open a hole. Jump up through the hole, then go to the right and go through the door there, then go through the door on the right to reach a large room.

Go to the right, then roll under the block and go to the right until you can go downward. Go to the lower area, but try to avoid hitting the Scizors below. Kill all the Scizors here, then go to the left, getting close to the wires without touching them. Run toward the right until you Speed Boost through some blocks.

In the next room, you will see a Missile Tank up above. Go to the far right side of the room and jump up to roll to the left into the water tank. Go to the left to get the Missile Tank. After you get it, jump up to the left and roll to the left to fall onto the Pit Block below.

Now go to the left to return to the previous room. Walk up against the left wall, then run to the right and you will Speed Boost through some Boost Blocks until you reach a door. Go through it.

You will be locked into this room. Kill the Scizor and it will turn into a Golden Scizor. Use the charge beam or missiles to kill it. The doors will open after that. Go through the door on the right. Then in the large room, go through the upper right door to reach the Recharge, Save, and Navigation rooms.

In the Navigation Room, Adam tells you to use the Data Room in PYR to get upgraded missiles.

Go through the door on the right, go up the elevator, then go to the Sector 3 elevator and go down.