It's now finally time to get the heck out of this place. Return to Chozodia by way of Crateria, picking up Power Bomb CR.01 along the way (you'll find the landing site in Crateria deserted of course, sniff) and proceed back into the Space Pirate Mothership. If you go back to the hangar bay you'll find the door still closed sealing you off from the scout ships, but there's still one more area that you haven't explored yet; the large seemingly empty room at the top of the ship.
Trek up to the bridge room, then once there save your game one last time to stock up on energy/ammo. Cross through the door up in the top right corner of the bridge room to locate a dead-end room. Lay a Power Bomb to open a hidden tunnel in the wall and crawl on through. The following corridor houses Energy Tank CZ.01, grab it if you haven't already. Beyond this corridor you'll find a small chamber divided in half by a large wall, use a Power Bomb to reveal the hidden tunnel leading through it. Upon clearing the wall, check your map.
The room right ahead of you is a dead-end, and appears to be empty. Shoot open the red door with a Missile and enter this last remaining room yet to be explored. You'll enter the darkened chamber which appears to be a totally empty maintenance room at first. The door seals behind you as you begin to hear a faint scraping sound. Remember the large green mechanical eye that opened up when you first entered the ship? You're about to find out what it belongs to.
Without warning a giant robot with the head and arms of Ridley comes clawing its way into the room before launching an all out attack. This mechanical beast is your last boss challenge, take this thing out and you'll be free to ultimately escape. Check out the bosses section for tips to short circuit this monstrous mechanical version of Ridley.
Once Mecha Ridley finally admits defeat and collapses in a heap on the floor, you'll think you've won. But this ain't over yet. As one last effort to defeat Samus, the eye on Ridley's head will flash red before the game alerts you that the self-destruct sequence has been activated. Uh oh. Now you've got only 5 minutes to get out of here before the entire ship blows itself into oblivion (you'll have only 3 minutes on Hard!). Grab all the health refills that appear above in the air then get the heck out of there.
Like lightning make your way back to the bridge, blowing open any obstructions and mowing down any Zebesians in your way. When you reach the corridor before the bridge where there's a shutter blocking your path, shoot up into the roof and crawl through the tunnel up there to bypass it. Once back in the bridge, quickly drop down and go through the door in the bottom right corner of the room.
Descend the following shaft while clearing out Zebesians (part of the floor in here can be blown open with a Power Bomb to act as a shortcut as you climb down). Make your way through the next corridors, clearing out Zebesians blocking your path. Eventually you'll reach the large room where a stupid maintenance droid blocks the way, shoot it with Missiles (or Super Missiles if you have any left) and wait for the slow thing to walk over to the right - you'll still have time to escape though, so don't worry about His Royal Slowness wasting time.
Head right from here and cross the next open room to find the narrow tunnel leading into the hangar bay. Roll through and drop down into the hangar. One last surprise awaits you down at the hangar door below - two black Zebesians are waiting in ambush near the door. Finishing both of them off can be tricky, try your best to avoid their attacks. On Hard mode it's a different story though, as they can quickly drain your health together.
Try to lure them up to the platform above the scout ships, and take them out one by one as they climb up after you. Use fully charged shots from your beam, three direct hits should finish each annoying foe. Watch their jumping patterns and try to avoid their annoying lasers. With both creatures fried the hangar bay door will finally open, ultimately guaranteeing your escape. Run inside to be greeted by a Zebesian as it jumps out of the scout ship to attack. Fry the creep and jump into the scout ship's open cockpit.
Now sit back and enjoy the ending as Samus flees from the doomed Mothership (and watch as a stupid Zebesian tries to stop you escaping). With Samus finally escaping the doomed Mothership, she'll have ultimately completed her mission and you'll have learned what really happened during her first adventure.
Upon watching the credits roll in their full, the game will go back to the giant Chozo Warrior's room. Watch as the camera pans down to the base of the wall, revealing a small engraving of Samus as a young child accompanied by two Chozo adults. Ain't that cute? You'll then be given a piece of artwork of Samus which is determined by your clear time and item collection rate, as well as the difficulty setting you've played the game on. Check the secrets and tips and game endings sections for tips on unlocking all the image gallery pieces, as well as the other unlockables and hidden tidbits in the game.
So that's it, with this guide you should successfully find all the items hidden throughout the game and make it in one piece. If you're playing for under two hours, I strongly suggest sequence breaking by picking up the Varia Suit and Screw Attack items early, check the secrets and tips page for details. If you've only played through on Easy, why not try Normal then Hard? And remember that sequence breaking thrives in this game, so there's plenty of ways to finish the game in absolutely insanely fast times well below 1 hour.