| Missiles | |
| 1 | Brinstar - After getting the Morphing Ball, enter the door to the right and fall to the bottom of the room. |
| 2 | Brinstar - After getting M-1, enter the pink door at the right, roll under the column and get M-2 |
| 3 | Brinstar - In the big pink room with the Charge Beam, right on the bottom left corner of the room. |
| 4 | Norfair - After getting the Hi-Jumb boots, enter the door to the right and jump to the top of the room |
| 5 | Norfair - From the main room enter the door on the top right, go through this room and at the bottom middle of the next room, hidden in the wall, in the lava is M-5 |
| 6 | Norfair - In the bubble room, head to the right side and shoot down. Fall down there and jump across the spikes for M-6 |
| 7 | Norfair - In the room with the enemies jumping from the floor, enter the red door on the right and jump across the platforms. |
| 8 | Norfair - In the room right before the Speed booster, shoot the ceiling two sqaures away from the door. |
| 9 | Brinstar - After getting PB-1, use a power bomb |
| 10 | Norfair - In the falling room, two after Crocmire, enter the red door on the right |
| 11 | Norfair - In the room before the grapple beam, hyper jump to the top of the room |
| 12 | Norfair - From the Crocmire room, go up the blue door, then up to the door at the top left and grapple across to M-12 |
| 13, 14 | Crateria - After getting E-5, Power bomb, go below the statue
and enter the door to the right.
Jump and quickly shoot. Use the Z-ray visor to find where the fake blocks are and stand over two and three. As you are falling, shoot both sides and get 13 and 14 |
| 15 | Crateria - Across from the Map station, enter the blue door, and follow the path |
| 16 | Crateria - In the old mother brain room, after killing the first Pirate, use the bombs and fall through the hole at the bottom |
| 17 | Brinstar - After getting PB-5, power bomb through the walls and enter the room after M-3. There is a fake enemy tunnel on the left. |
| 18 | Brinstar - In the room with M-3, use the grapple beam to get across |
| 19 | Brinstar - After getting RT-1, M-20 and 21, jump over the enemy hole and bomb the last part of the column, roll through. |
| 20 | Brinstar - After getting RT-1, power bomb and enter the tunnel below the statue. |
| 21 | Brinstar - After getting M-20, power bomb and get M-21 |
| 22 | Crateria - Use the grapple beam to land on the platform |
| 23 | Wrecked Ship - In the main room on the left wall, bomb the bottom most block. This is above the room with SM-4 |
| 24 | Wrecked Ship - At the top of the Wrecked Ship to the top right door |
| 25 | Crateria - After leaving the ship, use the green gliders to get to the top of the room. In the wall to the left is M-25 |
| 26 | Crateria - After getting M-25, fall down and find the Super Missile block. Hit it and fall through and head left |
| 27 | Wrecked Ship - After using the Chozo Statue to get to the bottom, bomb the floor and roll across. Then power bomb and jump up. Shoot the two drones into the pits and there it is |
| 28 | Crateria - After getting the Gravity suit, go to the bottom left of the room with M-25 and 26 and shoot to find a hidden tunnel. |
| 29 | Brinstar - In the room with M-2, Power bomb the column, then run and Hyper jump through the column. Enter the door, and jump up to find the invisible blocks. Run across them and enter the door. |
| 30 | Brinstar - After getting M-29, shoot down to the left to find M-30 |
| 31 | Maridia - After power bombing the pipe, enter the door at the top.The enter the door at the right. Shoot the door back open, open the shutter with a SM, kill the crabs. Then get a running start and right as you enter the door, hit down. Walk over to where the plants are at the bottom and Hyper jump up from the center of the left-most plant. |
| 32 | Maridia - After power bombing the floor, get a running head start and Hyer jump through the gap. |
| 33 | Maridia - Before getting to Botwoon, in the room with the fake spikes, just go across to the right side of the room |
| 34 | Maridia - In the room with E-11, on the right wall. Either use the Tatori, or stand on the nook, jump up and shoot down and fall down along the wall. |
| 35 | Maridia - It's in the room to the left of the elevator, run through the wall to your right. |
| 36 | Maridia - After getting M-35, enter the door to the left and follow the path through the hidden wall. See SM-9 |
| 37 | Maridia - In the room with M-32 and SM-8, shoot the fake blocks and the bottom right and enter the first quicksand pit |
| 38 | Maridia - In the room with M-32 and SM-8, shoot the fake blocks and the bottom right and enter the second quicksand pit |
| 39 | Brinstar - Before Kraid's Hideout, in the room with the four keyhunters, power bomb the right most wall and spring ball up to the missile |
| 40 | Norfair - Top left Green Door in the Bubble Room |
| 41 | Norfair - After getting M-40, Power bomb and use the raised column to enter the tunnel. Go across the room and the last block is M-41 |
| 42 | Norfair - In the room before the Ice beam, speed boost til you fall and power bomb. Go to the left and enter the blue door. In the left wall is M-42 |
| 43 | Norfair - Before the fight with the Gold Chozo Statue, jump across the fake blocks |
| 44 | Norfair - After getting the Screw Attack, go up then right.
When you enter the room the the yellow pirates and the faces, instead of entering the blue door at the top, shoot the ceiling and jump through. Go through the red door and fall down the left side to find a tunnel. M-44 is in a heart-shaped room. |
| 45 | Norfair - In the room with E-13, go to the top and across from the blue door at the top, the wall on your left is fake, run through and head to the top. |
| 46 | Norfair - After getting M-45, head left and enter the hidden tunnel below the red keyhunters. |