Time for our last romp on the Bottle Ship! Samus touches down in the main hangar, where the 07th Platoon's dropship is now absent. You're now free to explore every area of the Bottle Ship before locating Adam's memento. The game also informs you that Power Bombs can now be used (boy that would've been really helpful during the Queen Metroid battle!).
The map directs you where Samus wants to go - up in the control room where Adam previously coordinated the mission. You can also now see your item percentage rate in the pause menu, along with glowing blue dots all over the map, representing the remaining items to be found. It's unfortunate that the game gives away the location of the items so easily, but such is life.
For the sake of this walkthrough we'll travel through specific routes in each sector to find all the remaining items, but please be aware that you're free to explore the ship any way you want.
Begin travelling up north toward the control room, but pause in the long corridor with the broken elevator shaft (incidentally, this is the chamber where we saw MB murder all the scientists in an earlier cutscene). Clear the area and use the Speed Booster to reach Missile Tank MS.09 hidden up a tall shaft.
On the way here, you might have noticed that the cargo containers in the chamber where you first met the 07th Platoon are missing - the Federation must have helped themselves to whatever was worth taking before resigning the Bottle Ship to oblivion.
Keep moving onward toward the control room. Don't forget to pick up Accel Charge MS.01 inside the elevator chamber just south of the Navigation Booth (look through the glass wall at the top of the chamber). Travel beyond the Navigation Booth and save your game if you wish. Step through to the control room, where the area is now devoid of any activity.
We need to travel up to the overhead chamber where Adam commanded the mission. Exit the chamber via the door on the right. Before you can do anything in the next chamber, the doors lock and the camera focuses on a Power Bomb blast shield pod on the far wall. A note appears on-screen to remind you how to use Power Bombs. But hang on, those round metal shells housed a nasty Desbrachian during the earlier MB confrontation...
Ah well, at least there's only one this time. Deploy a Power Bomb to awaken it. Sure enough, the explosion dislodges the blast shield pod and summons an angry Desbrachian within. So all this time, we've been passing by these pods without realising that each one housed a deadly creature...
Desbrachians are quite hard to fight, even one-on-one. Check the mini-bosses guide for tips to handle them, and remember to Sensemove all the way to victory. Defeat the Desbrachian and the doors will unlock. However, the small elevator on the northern wall conveniently remains permanently shut. So we'll need to find another way to reach Adam's former command room up above.
As it turns out, each Desbrachian/Power Bomb blast shield pod covers a small hatch. Climb through the now-accessible hatch to find a new unexplored area of the Main Sector. Step through the following silent corridor to locate the sprawling Bottle Ship Residential Area. This multi-storeyed chamber once housed the human inhabitants of the Bottle Ship - now it houses a swarm of pesky Super Kihunters.
Clear out the swarm and take a look around. Use the Shinespark and Space Jump to successfully reach Energy Part MS.02 high above the central spire. Unfortunately you can't inspect the living quarters surrounding the chamber (or the small elevators connecting each floor), so depart the area via the northern exit. Step inside the civilised decor of the next corridor. Watch out for a pack of Cyclaws as they try to ambush Samus from the ceiling.
A Navigation Booth awaits at the far end of this corridor. Save your game there to unlock the door and allow progress. Step through the exit and shoot down more invasive Cyclaws in the following corridor. Beyond here is a pristine chamber housing an elevator transport - where does this one go?
Before stepping inside, check your map and make sure you've picked up all the items in the lower half of the Main Sector. Walk inside the elevator and ride it down to suddenly find yourself a few degrees lower in Sector 2.
This hidden elevator is locked inside a small chamber - the only exit is blocked by another Power Bomb blast shield pod. Here we go again - lay a Power Bomb to dislodge the Desbrachian covering the hatch. Conquer it to allow safe passage from the room. Step through the unlocked hatch to find yourself in the corridor leading toward Sector Zero. Samus was here much earlier, when the engines of the Bottle Ship roared back to life.
Feel free to explore what's left of the entrance of Sector Zero, but there's nothing significant to find there. Instead, step through to the big chamber where you fought Nightmare twice. Descend to the base of the chamber, only to find that Nightmare's remains are nowhere to be found!
The Federation must have cleaned up the mess... But remember - this game is a prequel to Metroid Fusion, and Nightmare originally appeared on board the Biologic Space Labs (BSL) research station in Metroid Fusion.... hmm... I think it would be a safe bet to say that the Federation has taken Nightmare's remains there.
Step through to the neighbouring Navigation Booth and save the game if you wish. Proceed through the gravity-affected corridors beyond, and pick up any items you might have missed before. Return to the freezer where the dead Gigafraug was always seen... until now. The Gigafraug has vanished, but two Baristutes still play around the room.
Do you remember the long chamber where two Missile Tanks were hidden up in a pipe running along the ceiling? It's to the south-west from your current position. An item still hides in that area, so travel down there to find a Power Bomb blast shield pod along the southern wall, beneath the cargo wall runner's railing. Lay a Power Bomb and defeat the resulting Desbrachian. Step inside the freshly-unlocked chamber to find Energy Part S2.02.
Now we'll travel to the northern half of Sector 2 and pick up a number of items there. Travel up through the long corridor where you received the Speed Booster, and return to the long L-shaped snow region near the main elevator of Sector 2. Proceed up north through the sector to the large ice cavern where you originally fell off a bridge and faced your first Gigafraug.
A trio of fireflies now hover in the air where the bridge once stood; simply fly across with the Space Jump (or use the trusty Speed Booster) and step inside the Navigation Booth. Save your game there if you wish. Move onward through the Sector Generator Room (remember, Fumbleyes are now vulnerable to your weaponry) and travel east to the long corridor where tall green specimen tanks line the chamber. A Fumbleye now inhabits the ceiling. Use the Wave Beam or a Power Bomb to clear out all enemies in this area, revealing Missile Tank S2.17.
With your latest Missile secured, travel through to the Experiment Floor where the rogue Groganch was found some time ago. A pack of Volfons now roam the snowy wastes, but are no match for Samus' might. Climb up to the northern end of the area to find that the Federation has retrieved Maurice's body from where he was killed (interestingly, the characters screen in the pause menu suggests that the Federation never found K.G. - we know by now that the lava had claimed him in Sector 3).
Step inside the glass tunnel (where you first spotted MB) and look for Missile Tank S2.18 hidden under the floor. Go through to the Materials Storehouse to search for Missile Tank S2.19 and Energy Part S2.03. Strangely, the Ferrocrusher vehicle that James used against Samus and MB is no longer resting in the corner of the chamber. Maybe the Federation thought it was worth salvaging?
No matter, let's keep going. Follow the path up to the cargo elevator and ride it down. Save your game at the next Navigation Booth if you wish, then make your way to the deep south-west of Sector 2 from here (don't forget to pick up the Missile Tank in the avalanche freezer if you missed it the first time).
Ride the Materials Transfer Lift cargo platform to the south (this time it's a completely uneventful ride), then move through to the chamber housing the five water tanks. A Power Bomb blast shield pod inhabits the western wall - you know what to do. Lay a Power Bomb to summon the Desbrachian, then defeat it and step through the hatch to locate Energy Part S2.04. That should be the last remaining item in Sector 2, so let's travel to the nearby main elevator and return to the Main Sector.