Leave the ruins and head back to the large shaft just after the last room containing lava. As you drop down the shaft, go through the opening on the right wall about halfway down to find a new area to explore. Go through the corridor to find a Save station and a hole in the ground. Save your game and dive in. Go down the huge shaft in the next room (watch out for the spiky bushes lining the roof) and go through the first opening on the right wall to face a Gamma Metroid. Once you've dealt with it shoot open the crumbling blocks in the floor near the door and head right.
In the next tall shaft, go up to the very top and jump up through the opening in the roof. You'll now be in a room full of honeycomb-type foliage, in here you'll face an Alpha Metroid on the right. Once it's gone use the Spider Ball to reach a small opening in the roof that leads to a Gamma Metroid. If you go through the opening on the right past the Metroid shell you won't be able to reach the Gamma Metroid, instead, jump into the Metroid shell and you'll fall through into a hidden tunnel. Crawl through the tunnel on the right to reach the room with the Gamma Metroid. Once you've dealt with it go back down to the large shaft.
Drop down and go through the opening on the right wall. Cross the next corridor, then drop down to the bottom of the next gargantuan shaft. Go left at the bottom then drop down to the base of the next shaft to face a Gamma Metroid. Once you've defeated it fill up your energy via the energy refill ball at the base of the shaft, then ascend the shaft and head left. Climb up the next shaft and go left through the opening near the top.
In the next corridor you'll see an Alpha Metroid on the other side of the wall, it'll become a Gamma Metroid and try to break through the wall to get at Samus, but of course it can't get through. Go left and jump up through the Metroid shell to reach it. Once it's dead, go left to find a tunnel leading back up to the first long shaft. Once back up there, climb up and head through the door on the left. Cross the corridor to face another Gamma Metroid. Once this one's defeated an earthquake will occur, so it's time to retrace your steps.
Go left past the Metroid's shell to find a path leading back up to the previous shaft. Once there, go left and you'll find a room filled with lava, so you'll have to come back here later. Leave this area with the funky music to return to the large cavern where the lava was previously. The main theme will begin playing, head left and drop down where the lava used to be. Down the bottom of the next shaft you'll find more lava, so cross over the platform and go left past the Metroid shell.
The music will change in the next room, from here traverse through the next few tunnels and shafts to eventually face a Gamma Metroid. Once you've defeated it an earthquake will occur, so you'll now have to go back to the previous lava area you saw just after leaving the area with the funky music.
Once you reach the shaft where the lava dwelled, drop down to the bottom and head left (watch out for the spikes). Ascend the next shaft, eventually you'll find two Metroid shells and two separate paths, one leading left and one straight up. Go up to eventually find a Gamma Metroid and a missile refill pod, through the left opening you'll find an energy refill ball and an Alpha Metroid. Once you beat both Metroids you'll experience yet another earthquake, more lava's now cleared away. Leave this area with the funky music and head back to the area playing the main theme.
Go back to the area that previously contained lava (if you can't remember where it is, check out one of the game maps), and head down the now-empty shaft. Travel down the corridor at the base of the shaft to the left, in the next corridor beyond it you'll find a blocked-up wall. Use Missiles to break through the two large blocks, then head left over the top of the lava. Ascend the shaft beyond the lava and head left at the top. Climb the next shaft and go left. In this next corridor you'll face a Gamma Metroid, once it's dead go through the opening on the left to find the biggest - and last - of the ancient ruins.