When the player begins this level for the first time, the first cutscene plays. It shows Zero Suit Samus breaking into the Research Facility through a ventilation duct. After defeating a few R.O.B.s (mostly R.O.B. Sentries) she encounters Pikachu who is being harnessed for his electrical power. She breaks Pikachu out, which sets off many numerous alarms on the Isle of the Ancients. R.O.B.s come swarming in and Zero Suit Samus and Pikachu defeat them. Right before the stage is cleared, you will see a cutscene of Zero Suit Samus staring at her Power Suit.
When the player begins the player must play as either Zero Suit Samus or Pikachu. He will find himself in a room filled with technical boxes. Break the boxes to get through. After breaking the boxes, the player should find a Door. After he enters the door, He will find himself in an area with an Elevator. He can move the elevator up with the jump button, and down with the crouch button. Go down to the bottom to find some R.O.B. Sentries, and an Orange Cube. Go up past where you started and up again to get to the higher part with the Door. Run right to find the door. Defeat the enemies in your path. Now all you must do is enter the door. Inside you'll be in an area. Run right to find some R.O.B.Sentries, two R.O.B. Blasters and another Door. Defeat all the enemies and enter the Door. You'll find yourself in a room. Run right to find a giant wheel of rotating platforms and two R.O.B. Sentries below it. Don't go on it, instead go past it and jump on the higher part of floor in which an orange arrow is pointing. A R.O.B. Blaster should meet you there. Defeat it and go down the green ladder. Enter the Door down there. Inside, run down the floor and jump to a large platform with other platforms above it. You will enter a forced battle against R.O.B. Sentries, and two Roturrets, which are above the platforms above the large platform. After all enemies are defeated, jump on the platform next to the platform you were on and onto the floor. Now run up to find a lower part with some treadmill-like thing that pushes you forward and a higher part with a locked Door. Go down the lower part and either run there or take the thing that pushes you forward. You will find yourself (running)/ land (taking the thing that pushes you forward) in an area with some R.O.B. Sentries, a platform with a Key, and a Buckot above that platform. Defeat the enemies and take the Key. Then run back to the part with the lower part and upper part with the locked door. Avoid the the thing that pushes you forward by jumping over it. Now jump to the upper part with the locked Door and run into the Door to unlock it. Of course, you can throw the Key at the door, but because the Door is on the upper part, which is going up diagonally, you cannot throw the Key or you'll lose it. Now pass the locked door's area to find a lower part and two upper parts. The upper part on the left has another locked door. This time the lower part is on the left (the other one is on the right). Take the thing that pushes you forward (or run) to a part with a Roturret and two R.O.B. Sentries. You don't have to go here if you don't want to, since no Key is here. Run back to the part where all parts meet (two upper parts and lower part). Run up the upper part on your right. A RO.B. Sentry will meet you here. Defeat it, and continue moving. You'll enter a wide room with a Roturret nearly touching the ground. Defeat the Roturret and move on. Take the thing that pushes you forward, to enter an area with the Key, and an Orange Cube. Now jump, double jump and up-special back to the part in which you were pushed forward, and run to the upper door. Like the previous locked Door, you must run into the door to unlock it, because if you throw the Key, you'll lose it. Now run pass the locked door's area and over a platform with rails on its sides, and a light brown/yellow color. Run across the platform and hit the switch on the run. The platform you just ran across will move forward, and then upwards. You can see its path. Now run back to the Door, in which let you in this area. An orange arrow will help you get back to where you started in this area. Exit out of here. When out, climb up the green ladder, and either take the rotating platform wheel, or jump, double jump, and up-special to get to another part on your right, in which an orange arrow is pointing. Defeat the R.O.B. Sentry in your way, and enter the Door. You will be in an area, in which, the same platform that went upwards when you hit the switch in the lower part is in front of you. Run on the platform. The platform will move east. Avoid the Electric Jyks during the ride until the platform collides into a wall. As soon as it does this, you will enter a forced battle against two Glunders. Hit the switch that appears to make a floor appear, that leads you back to the door you just came into. Exit out the Door. Take the rotating platform up to a green ladder. Climb the green ladder to reach the highest parts of the area. Go right and break the boxes to find a secret Turquoise Cube. Go left now, past the ladder to find a R.O.B. Sentry. Defeat the R.O.B. Sentry and jump over an opening in the path. Jump across to find another R.O.B. Sentry. Defeat it. Now the path fall down (not much of a fall) a small part of the part with the defeated R.O.B. Sentry. Enter the door there. You will enter an area, with a waterfall in the background, and infinite number of Bytans and two R.O.B. Launchers. It makes no sense to defeat the Bytans, as for, your only fooling yourself because another one will always fall. So, ignore the Bytans, climb up the ladder on the ground, and jump to a purple platform. Now jump to another platform attached to the wall on your left, then another one on your right. There are two R.O.B. Launchers on these platforms. Defeat them, otherwise they'll shoot missiles at you. After they are defeated, jump to a higher part of ground. More Bytans will fall to the ground, and the amount of them is still unlimited (there will always be more when they are defeated), A platform on your left has a Turquoise Cube. Usually, it gives you Food when broken. Eat the food to reduce your Damage percentage. Jump from the platform to another platform with the door. Inside run forward and jump to a high platform with a Turquoise Cube containing a Heart Container. At first everything is safe and sound, but as you jump off this platform, to ground, then to another platform, three Giant Bytans fall to the ground. These guys are ten times bigger than normal ones, and have more health. They are super strong, and can easily KO a player not paying attention. After all three Giant Bytans are defeated, you'll enter an area with many Quark Mines. Avoid the Quark Mines until you reach a platform. You'll enter a forced battle against Metal Primids (usually six). After all of them are defeated, run and jump to a high platform and enter the Goal Door at the end.
- During the entire level until you reach the part with the Bytans, Metal Primids and Giant Bytans- Opening/Menu (Metroid Prime) plays.
- Inside the parts with the Bytans, R.O.B. Launchers, and Metal Primids- Multiplayer (Metroid Prime 2) plays.
- R.O.B. Sentry
- R.O.B. Blaster
- R.O.B. Launcher
- Giant Bytan
- Metal Primid