Phase 2
The Bombs
After dropping off from the save station, head straight right. You'll come to a cave that was covered in lava before, but now, it's cleared off. Head down the cave. You'll reach a hallway with a lava pit to the far right. Remember this area. Continue right.
You'll eventually come to a fork. For now, take the upper path. Once you made it up there, go straight right, avoiding the Chute Leeches (pancake thingies) and the Gulluggs (the long beak things that do major damage). Head down the area, and then, on the bottom, left past a hallway. Break the item sphere to find the Bombs. These things are literally bombs. Drop them with 
while in Morph Ball. Don't worry about supplies; you have infinite.
Put these things to the test by placing them on the floor below the Item Sphere. Get your first Missile Expansion. This comes in useful, since Metroids need missiles to be killed and you'll need lots'. In fact, if you want to win the game, 150. On a side note, Bombs can help you get out of a hole or get into a tunnel that can't be normally accessed. This will be explained later. Jump out and head right.
Once back in here, climb up. This time, head to a hallway on the right. As you progress, you'll find it's a dead end. Let's disprove that. Kill the bird-like shooters here and climb on top of of it Place a bomb, and hold the dpad right. You'll burst into the air, and because of the dpad, you go right, revealing a secret hole. Continue right, bombing any obstacle in the wall.
Energy Tanks and Ice Beams
Upon exiting the wall, you'll find an Energy Tank. You'll want these. When your normal energy runs out, it'll then switch to that Energy Tank's energy. So, technically, you have an "extra life." So, the more the better. Snatch it and move on.
You'll find another area leading down. Drop all the way down. Then, go left. You'll then find yourself with another nifty item: the Ice Beam. Unlike your normal beam, it freezes enemies. Thus, you can now use them as platforms, to pull yourself up. It also helps to kill enemies. Freeze it, then kill it. Leave and head up until you find a hallway that goes right.
Missile Expansions
There are 3 Missile Expansions here. Kill the enemies blocking it, then get yourself inside. For the first, shoot the blocks (jump for the upper one) and get inside. The second; not so much. Destroy the lone block, and jump at the exact moment the block comes back. This is tricky, and if you can't do it, then come back when you get the High Jump Boots. The last one is simple; get yourself up, and shoot down. Leave when done, and climb until you find a hallway to the right. Avoid enemies and continue right.
Bomb, then morph ball your way into the right one and get the left one like we did with the second. Head right and go down to find an alcove in the wall on the right side. Continue heading right. Soon, you'll fall down a hole.
Spider Ball
Maneuver and morph ball your way down. At the bottom, you'll find a most nifty item; the Spider Ball. Like its name, you can climb up walls like a spider. This extremely useful, and you can be lazy and climb up walls with it! But soon, you'll realize you're stuck down here. This isn't a problem for your new item. When in Morph ball mode, press to enter Spider Ball mode. Then climb up, up, up, until you reach the surface. Press 
to go to your default ball form.
Once back up, jump over the hole you came. Then Spider Ball your way right and keep going. Don't stop for anything. Soon you'll be on the right wall of the big, central area. Keep going until you reach a alcove. Go through there.
You'll find a hallway, where a Metroid resides. Kill it and, Then go to the back wall of this alcove and simply continue to move on the wall. You'll eventually leave and arrive on the ceiling. Watch the enemies here. There's a health and missile restock area here, protected by enemies. If you desperately need it, go ahead. If not, drop down. Head left until you see a small cliff. Drop and head right, bombing the tiny bush thing. Continue right. This room may seem like deja vu, but you'll see 2 Missile Expansions ready for you to take. Exit.
Metroid Killing
Head straight right back to the tall fork we saw in the start. Take the lower path, and head right at the bottom, breaking and bombing your way through Then drop down and go right. Kill the Metroid here. Then go left and drop down and take either path, then take the other. They both have a Metroid, so go whichever way you want. Then you'll hear the earthquake, so leave this section.