After you witness the carnage wrought by Metroids in Tourian, you battle Mother Brain.

Reach Mother Brain

Turrets will shoot beams and rings throughout the battle. You can Screw Attack to destroy them, or just move out of the way if you can.

There is a glowing glass barrier to the left. Shoot missiles at it repeatedly to make it keep shrinking until it disappears. Go past where it was. Continue destroying glass barriers until there is a solid wall to the left with a small tunnel at the top. Then jump up and grab the tunnel and roll through. You will find Mother Brain.

Defeat Mother Brain

If you need to refill missiles and health, you can ignore Mother Brain and shoot the rings that come out of the turrets on the right until you're ready.

The only places where you can safely land are the two small blocks above the lava and the upper-right corner of the area. Do your best to jump well and dodge the rings and beams from the turrets.

If you haven't already, use Missiles to destroy the glass around Mother Brain.

With the glass gone, Mother Brain will sometimes shoot a beam of energy out of its eye at you. Carefully jump over this.

Escape

After you destroy Mother Brain, a 2 minute self-destruct timer begins. Go to the left through where Mother Brain was, and go through the door. Jump up through the room, but beware that most of the blocks in this room are slow Pit Blocks that you will fall through if you stand on them too long.

At the top, take the elevator up to Crateria. Go through the door on the right and make your way up the room, then Screw Attack through the walls on the right, but before you go through the door, go to the left edge of the ledge and start running to the right while shooting. This will make you Speed Boost through the wall on the right so you can reach your ship. Jump up onto the glowing platform in the roof of your ship. There will be a cutscene, and you will end up in Chozodia.