Upon starting the game you'll be treated to a voiced intro narrative against a starry backdrop, then the weird looking Pirate Frigate comes into view. Samus' ships glides up to a landing platform, she then jumps out and we get a full 360 degree camera view before taking control. But what's this? Samus already has several of her upgrades, such as the Varia Suit and Charge Beam. Surely this must be too good to be true? (it is).
Anyway, take some time to get used to directing Samus around, and take note of the on-screen hints along the way. When you're ready, go over to the blue force shield and blast all four of the large red buttons to disengage the field. In the next area, switch on the Scan Visor (D-Pad left) then scan the button on the pillar.
Now there's power going to the force shield activation switches, fire at all six buttons to open the field. Jump up to the next platform and head over to the airlock door up the ramp ahead.
Once inside, get out your Scan Visor to pick up various information of the Pirate's activities and dealings. Go through the first tunnel and head through the door at the far end. The atmosphere becomes far creepier in the next room, where you'll find debris and dead parasites floating around. Scan the button on the wall to repressurize the room and power up the door at the far end of the corridor.
The next corridor's riddled with damage, while several parasites crawl around under the floor, something fishy's definitely going on here. Go into the next room to meet an incredible sight. This room, once an evacuation assembly area, is now filled with dead Space Pirates and the carcass of a massive Parasite Queen, this sight's not for the faint-hearted.
Head through the room scanning everything to learn more about the events that befell the Pirates, and don't forget to scan one of the live Parasites for your log book. Head around to the other side of the room, where you'll find a weakened Space Pirate, fry it before taking any damage. If it drops health, scan it for your log book.
In the following tunnel your passage is blocked by ruins from the roof. Blast it open with the Charge Beam and head through. In the next room, you'll see a pack of Parasites sneaking down a narrow tunnel. Follow them using the Morph Ball to fit, and you'll find a room with a Map Station. Scan it first for your log book before downloading the map.
Go back out to the corridor and head right to find an elevator leading down. Scan the button and walk into the hologram that appears to ride down the shaft to reach Deck Beta. Use the Morph Ball in the next corridor to make it through all the rubble and watch out for the arcing electricity. The next room has more gruesome sights to behold, a second Parasite Queen appears to be hibernating inside a giant cryotube.
You'll find two more injured Pirates in here, but they'll be no match for you of course. Scan around to find more information on the Pirate's research, then head through the door on the far side of the balcony. Watch out in the next corridor, as an Auto Defense Turret's just around the corner. Scan it then blow it apart with a single missile.
Go through the door below the remains of the Turret to find an elevator, scan the button on the wall and walk into the hologram to ride the elevator down. The next huge room's full of information waiting to be scanned. Scan the console on the left to disable the turret ahead, then scan the consoles around the cryotube containing the mutated remains of a Parasite Queen, one of them contains the Fall of Zebes Pirate Data.
Once you've finished scanning (and reading), go up the elevator beside the cryotube. Head around the upper balcony while taking out wounded Pirates along the way. Head through the next corridor to reach a long sloping elevator shaft. Take out the Turret there and ride down the elevator shaft to Deck Gamma. At the bottom on the shaft a Pirate drops down to confront you, fire a missile or two to knock it down.
You'll now need to open up the large door ahead. Scan the console on the wall to power up the locking mechanism on the floor, then activate the Morph Ball and roll into the slot to open the door. The next room's filled with more dead Pirates, as well as two Turrets. Blow the Turrets away and use the Charge Beam to draw in any pickups they leave. There's a save room next door, head in and save the game now.
An identical locking mechanism locks the door ahead, so do as before to open it. You'll now be in the huge main Reactor Core of the ship, surrounded by more dead remains of Space Pirates, and you're about to find out what's been attacking them. Walk forward into the main part of the room to meet your first boss encounter - a live and deadly Parasite Queen. Refer to the bosses guide to cook its hide.