With your fully-powered suit restored, we can now finally look for a way out of here without delay. First things first, we'll pick up a few items in the ruins on our way back to the Mothership. Save your game below before moving on if you wish. Now there's only one way out of here - through the water. Break through the Missile Block platform covering an access point to the water and take a dip.
With the Gravity Suit you'll have no more trouble moving around underwater. From here go and pick up Super Missile CZ.01 in the right corner. In this room you can also begin a Shinesparking trek to Energy Tank CZ.03 in the tall shaft beyond as well. But don't underestimate it, this item's probably the toughest one to reach in the game courtesy of the layout of the terrain and the trickiness of Shinesparking.
Once you're ready descend the tall shaft you'll recognise from earlier on. On the way down be sure to pick up Missile CZ.01 as well. Descend to the very bottom of the shaft (wasting stupid Zebesians along the way) and go left at the bottom. Proceed through the next large lava-filled room and be sure to pick up Super Missile CZ.02 in the corner. With that item in hand go left. You'll fall into a shaft where the laser alarms reside, don't worry if you trip any of them.
Head left at the base of the shaft and swing down to the lower door in the next room. You'll recognise this next room as the one with a shutter blocking your path. Here you can blow through the floor to discover Super Missile CZ.03 hidden below. From here backtrack to the Mothership the same way you came in and be sure to save along the way.
Upon reaching the long glass tunnel connecting the Mothership to the ruins, go back inside the ship and ascend the tall shaft filled with Zebesians. From here make your way back to the nearest Save Room. But watch out for black Zebesians along the way, they appear to be immune to your weapons but you'll need to pummel them hard with your Beam before they blow. Also watch out for small balls floating about releasing electricity, the only way to destroy them is with the Screw Attack.
Once back in the Save Room, save your game and head right. Proceed through the small chamber to find yourself back in one of the numerous tall shafts. Screw Attack your way up to the very top to find Super Missile CZ.04 at the apex of the shaft. We'll now go and find your first Power Bomb - the same one that nasty Zebesian extracted from the ruins. Exit this shaft via the only door along the right wall and proceed through to the right side of the following shaft (watch out for black Zebesians). Blow open the red door on the right wall and go inside to locate the hangar bay - you've been here before.
A door blocks your path to the scout ships ahead, so you'll need to find a way to open it. Climb up to the top of the room for now and crawl left through the narrow tunnel in the ceiling. Cross the next room and waste the two black Zebesians while trying to avoid their huge jumping patterns and green lasers. Beyond here you'll find a gigantic twisting chamber. Make your way over to the left side of the room and be patient as the maintenance robot blocking your path slowly walks forward to clear the way.
Descend the next shaft while clearing out Zebesians, at the bottom you'll spot a yellow door on the right which can't be opened without Power Bombs. Head left and make your way through the next corridor by way of the narrow tunnels. Keep following the next few corridors and shafts filled with Zebesian patrols, eventually you'll reach what appears to the ship's bridge (there's a range of huge windows on the left wall looking outside).
Once here you won't be far off your first Power Bomb. Go over to the bottom left corner of the room and drop down the narrow hole you'll see there. Roll down through the twisting narrow tunnels below to find yourself at the top of a room where the Zebesian that stole your Power Bomb lurks. He'll walk off into the room on the right, follow him down there to discover Power Bomb CZ.01 resting between two tall laser trip wires.
Space Jump over the top of them and fall down to retrieve your first Power Bomb. Try one out to open up the yellow door on the right, then go inside to retrieve Power Bomb CZ.02.
Keep in mind that your Power Bomb supply is low, and the only way to refill them is via the Save Rooms (those stupid Zebesians never give you energy or ammo refills!). Backtrack up to the bridge room, then from there you can go and pick up Energy Tank CZ.01 if you wish, but if you want to save time leave it for later. By the way, if you're not going for a 100% item rate, feel free to head up to the large room at the top of the Mothership now seeing as you're already nearby. But as this guide directs you to find all 100% of items, we'll head back down for now.
Save your game to refill Power Bombs just off the bridge before backtracking down into the bowels of the craft. Upon returning to the shaft where you spotted the yellow door, blow it open with a Power Bomb and go inside to find Super Missile CZ.05 hidden within the dividing wall. Pick it up and blow open the green door on the right. Descend the next shaft and go through the red door. You'll be back in Super Missile CZ.04's shaft.
Descend to the very bottom and go left. You'll be in a shaft full of searchlights, it really doesn't matter if any touch you. Drop down to the base of the shaft and go right. In case you're wondering where we're going, there's a couple of items near the entrance of the ship below. Lay a Power Bomb to break open the floor in the next shaft and go right through the door below. You'll now be back in the first large room filled with laser trip wires.
Walk through the one ahead and go through the door down on the left. From here make your way back down to the Save Room below. Recharge and save before continuing on, then go into the Map Room and blow open the red door on the right. Clear out the two Zebesians in the following corridor, you can then find Super Missile CZ.06 up above the cracked block in the ceiling.
Go outside via the green door on the right and trek back to the right end of the ship - the first part of it you saw after Samus crashed. Grab Power Bomb CZ.03 hidden in the side of the ship then go back inside by way of the narrow tunnel behind the Power Bomb. Once back inside return to the ruins and remember to save your game along the way.
Exit the Mothership and make your way to the large glass tunnel connecting the ship to the ruins. Lay a Power Bomb to shatter the glass and open up access to the rocky area below. Blast the Zebesians and head down to the bottom right corner of the cliff. Blow open the wall with another Power Bomb and go inside to eventually find Power Bomb CZ.04 up a tall shaft. With that in hand, go back up to the remains of the glass tube and descend the cliff down to the bottom left corner.
Blow open the wall with yet another Power Bomb and go inside to find a hole in the floor. Fall through to find a hidden shaft below. Screw Attack the electricity balls floating about and head right at the bottom if you wish to save your game. Go through the left door at the base of the shaft to locate a large room sloping upward, filled with small red creatures which you'll recognise from Kraid's area.
From here you can use the open space to build up the Speed Booster's charge to reach Energy Tank CZ.02. With that item secured, go back down the shaft and up the ramp to find another small shaft. Go left again to find yourself in a small chamber with a low ceiling. Up above in in the ceiling you'll discover Super Missile CZ.07. Leave this room via the left door to find a huge room filled with twisted platforms packed together in the ceiling.
Concealed within the mess is Super Missile CZ.08, grab it before moving on. Go left upon retrieving the item to find a long green corridor. Run through to find yourself back in Crateria's eastern side, where yellow doors had originally stopped you from entering Chozodia. Go left and blow open the yellow door with a Power Bomb. You'll now find yourself back in the watery cavern filled with Skultera swimming about below (this is where Missile Tank CR.01 was). Go left until you see an opening up above, then Space Jump up through the open hole in the ceiling.
Up above you'll be in the huge open area in Crateria's north-eastern expanse. Space Jump up to the yellow door and blow it open. Go inside and cross the long corridor to find yourself back in Chozodia. From here you can find Power Bomb CZ.05. In this same room, shoot a Missile into the floor at the right end to uncover a hidden tunnel leading back into the main area of the ruins. Before going back to Crateria, make your way over to the tall shaft in the ruins adjacent to the large watery room near the Chozo Warrior's room (destroy any huge obstructions you find with Power Bombs).
From there you can now find Power Bomb CZ.06. With both items secured return to Crateria by way of the upper connecting corridor. Run back into Crateria to charge up the Speed Booster, then quickly Space Jump up above to find Super Missile CR.01 behind a wall. Go back into the long connecting corridor and charge up the Speed Booster again to reach Missile CR.03.
From here we'll now return to the main areas of Zebes to pick up remaining items. Go back down to Norfair but before you pick up the remaining items here, go down to Ridley's area. Pick up Missiles RI.12 & RI.13 before returning to Norfair. Back in Norfair pick up Missile NO.08, Missile NO.13, Super Missile NO.02 and Power Bomb NO.01. We'll now take a hidden shortcut across to Kraid's area to save time.
Climb up to the apex of the shaft outside the Map Room and stand atop the single floating block. Shoot a Missile at the left wall to uncover a hidden opening and crawl inside. Blow open the platform blocking your path with a Power Bomb and go through the tunnel to sneak into Kraid's area without having to trek all the way around to the main elevator in Brinstar. Pick up Missile KR.09 to clear this area out, then return up to Brinstar.
Head back to the spot where you started the game and lay a Power Bomb to reveal a hidden Morph Ball Launcher below the platform. Use it to shoot up the shaft above. You'll now be back in Crateria, near the landing site. From here make your way over to the Tourian elevator you used to escape from here earlier. Ride it down to find the completely desolate remains of Tourian.
Descend the escape shaft and go back into Mother Brain's lair (there's not much left in there), then from here you can pick up Power Bomb TO.01 and Missile TO.01. With these last two items in your possession, you should have totally cleared out every item in the entire game expect for a Power Bomb in Crateria (and an Energy Tank in Chozodia if you haven't picked it up yet).