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Chapter 7: The Haunted Ship
The water heavily hinders Samus' movement.
Once you've finished Crocomire, go over to the left side of his corridor and enter the door there. From here you'll be able to find the Grappling Beam. Once you've found it, you'll be able to find a load of items before leaving Norfair to head topside to the Wrecked Ship. You should be able to pick up the Wave Beam, missiles no. 4, 5, 7, 8, 9 and 11 (Norfair).
You can also find Reserve Tank no. 1 (Norfair), Power Bomb no. 1 (Norfair) and Energy Tank no. 2 (Norfair). On the way up to Crateria in Brinstar, you'll be able to find the X-Ray Scope. Once you've found everything, go up to the main elevator in Brinstar up past the orange shaft. Go up into Crateria, go up the rocky shaft, then head right to find the room containing missile no. 2 (Crateria).
Cross the room using the Grappling Beam, then go out to the massive open area through the right door. On the far right of this area is the main entrance to the Wrecked Ship. Cross the platforms above the water, you'll need to use the Grappling Beam to swing across a number of them, you'll also have to grab onto a Ripper to swing across one.
Watch out for ghosts and spectres aboard this lost vessel.
Once you reach the other side, blow the door open with a Super Missile and enter the derelict ship. The first thing you'll notice inside is that the power's off. Run to the end of the long corridor and head through the door. Go down the main shaft to the very bottom, keep in mind that you can grab missile no. 1 (Wrecked Ship) on the way down. Once you're ready, go down to the very bottom of the shaft and shoot open the floor below (watch out for the Covern that appear).
Drop down through the passage and go through the door in the floor below. In the next corridor below, go over to the right-hand side, blow open a hole in the base of the wall to find a boss guard door. Destroy the door when the eye opens, then head through to face the phantom boss Phantoon. Refer to the bosses guide to send it back to wherever it came from.