The level begins with Zero Suit Samus and Pikachu going after Samus's power suit, which was somehow captured by the Subspace Army. Upon arriving at the room where the suit is stored, the duo are ambushed by two Shadow Bug clones of the Power Suit. After the copies are defeated, Zero Suit Samus uses her Plasma Whip to break her suit out of its glass container. By breaking the glass, however, she set off numerous alarms, and R.O.B.'s swarm the room. After defeating the enemies, Samus put on her suit and the duo sets off again.
Eventually, after a rather difficult maze of platforms, most of which are moving, they come to a large room where they are attacked by Ridley. The boss swoops down and grabs Samus, scraping her against the wall as sparks fly off the power suit. He drops Samus only when Pikachu jumps up and zaps him with Thunder. Samus and Ridley land next to Pikachu, and Samus's suit is still giving off sparks as though it is malfunctioning or damaged; nevertheless, she emerges unscathed in terms of damage. Ridley was covered in electricity when falling, though he only seems to give himself a headache when he lands face-first. He too looks unscathed. A boss battle ensues.
After defeating Ridley, the pair exit the Facility and appear on the grassy surface of the Isle of the Ancients. Samus spots R.O.B.'s carrying Subspace Bombs into another building, so they decide to pursue. This leads to the next level, the Subspace Bomb Factory.
- At the start of the level, Vs. Parasite Queen plays.
- During the False Samus fight and cutscene, Sector 1.
- When Samus puts on her Power Suit in the cutscene and the following part of the level, Theme of Samus Aran, Space Warrior plays.
- In the part with the teleporters, Main Theme (Metroid) plays.
- During the fight with Ridley, Vs. Ridley plays.
- The clone Samuses are similar to SA-X from "Metroid Fusion" and Dark Samus from "Metroid Prime 2 and 3".
- The background of this stage when fighting the Samus clones is one of the Stage Builder backgrounds.