At the beginning of the level, Zero Suit Samus is shown breaking into the Research Facility though a ventilation duct. After destroying a few R.O.B.s (mostly Sentries), she encounters Pikachu, who is being harnessed for its electrical power. She breaks Pikachu out, which sets off many of the numerous alarms on the Isle of the Ancients. R.O.B.s come swarming in, and Zero Suit Samus and Pikachu destroy them. After a rather confusing journey through the facility, and a cutscene of Samus staring at her Power Suit in a security room, the stage is clear. Zero Suit Samus and Pikachu will then join the player's team.
The first area of the level is very straightforward and very short. You go right and find an elevator. Go down to find the orange cube. Go up to continue your level. After the player gains Pikachu, however, the level takes a far more confusing design. The level branches into three paths from a single large room (containing a rotating platform wheel such as those found in the Stage Builder, but two of the paths cannot be traversed until the player traverses another specific path. In the first path, started from the bottom-right corner of the fork-room, the player commands a large platform-like vehicle to move to an area in the next path. In this path, accessed from the far right of the fork-room, the player rides the vehicle from before across a large gap to a switch, which causes large, jagged blocks to fall from the path above. In the final path, accessed from above the rotating wheel in the fork-room (and also featuring an indoor waterfall), the fallen blocks, previously acting as a wall, can now be used as platforms to reach the end of the level, but are strewn with dangerous Quark Mines.
- During the first part of the level, Opening / Menu (Metroid Prime) plays.
- After the 4 door hallway, Multiplayer (Metroid Prime 2) plays.
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