Say goodbye to the last ruins area and head back down to where the lava formerly bubbled and frothed. Descend the large shaft and head left at the bottom. Cross the next lava-filled cavern, then drop down the next shaft. Cross the lava in the next corridor, in the next room you'll find an area with an exit leading left and a path leading up. Go up the shaft to find a path leading left and right.
Follow the left path, you'll climb up a shaft and reach a corridor with the lower part filled with lava. Here you'll find a simple Alpha Metroid, it's a bit of an insult having to fight such a simple form after taking on the Zeta Metroids, but something ugly is still waiting in this room.
An earthquake will occur, but this time it'll be bad news. When you head back down to the shaft below, you'll notice it'll have filled with lava. Go up the right path leading back to the room where you fought the Alpha Metroid, but this time it won't be so easy. When you reach the point where the Metroid shells are, you'll spot a Zeta Metroid evolve into the massive Omega Metroid form.
This will be the toughest type of battle against the five main Metroid types, so you'll need to use skill to beat it. It won't be as fast as the Zeta Metroid, but it'll fire out electric sparks everywhere, so try to stay clear.
You'll need to pound it in the face for quite some time before it blows. Once you send it packing another earthquake will occur and you'll be able to head back down to the main shaft. Go back to the shaft and drop down to the bottom where the opening in the left wall is. Drop down the next shaft and cross the sea of lava. Climb up the next two shafts to reach a Save station.
Save your game here, as you'll have three more Omega Metroids to deal with. You might have to backtrack to reload your missiles before facing the Metroids as they'll take a pounding before exploding. Ascend the huge shaft and go right at the top. Go up to the top of the next shaft and head left. Cross the corridor over the pillars, at the end you'll find a room containing an Omega Metroid.
Once you've wiped the floor with it, go back to the shaft past the corridor and go through the door on the right side of the shaft. Cross the corridor with the pillars, and bypass the giant hole in the floor. Keep going right, in the next shaft you can save you game at the Save station at the top. Once you've saved the game, drop down to the base of the shaft and go right. In this next shaft blast the enemies here to often receive large energy balls, once you've regained your health go right about halfway down the shaft. Cross the pillars in the next corridor, you'll face the second-last Omega Metroid in the room beyond.
Once you've dealt with it, go back to the shaft and head through the door at the base of the shaft. Go left through the corridor filled with pillars to face the final Omega Metroid. The destruction of this Metroid means that you'll now be able to take on the Metroid Queen in its lair. Go back to the long corridor with the giant hole in the floor and drop down.