The room is entered only once, from Hive Chamber B in the Splinter Hive. Samus Aran follows a blue being resembling her Power Suit through a Dark Portal and ends up in this location. She immediately falls into a Safe Zone and finds Dark Samus absorbing from a wall of Phazon. The room seems to be sealed in with the ceiling open to the sky of Dark Aether and Phazon on part of the wall. Several mysterious creatures lurk around the ceiling, awaiting a meal. As Samus is about to get up, Dark Samus realizes someone is there and shoots, but misses. Samus is about to get up to combat Dark Samus, until the Light Crystal protecting her Safe Zone is destroyed. Dark Samus did this to get away from the Ing, even if she had to leave the precious Phazon behind. The Safe Zone then begins to flicker and shrink, and Dark Samus flees as the odd creatures leap down and prepare to go in for the kill. Samus continues to back away until the Ing jump on her, and she is knocked back through the Portal. After escaping, the Portal disappears, and Samus cannot access it anymore.
The Space Pirate Logs entry "07.159.9 (Two Hunters)" reveals that one of the Space Pirate scouts witnessed the incident here. This helped them to determine that the two Samuses were not allies. It was suggested that the Pirates propose a deal with Dark Samus, where she would be rewarded with Phazon if she killed the real Samus.
- The Portal Site, Subchamber 5 and the Control Tower are the only rooms in the entire Metroid Prime Trilogy to be completely unplayable, and later inaccessible as well. All only appear in cutscenes.
- Unlike the rooms mentioned above, the Portal Site is not present on the in-game map. Despite this, the room's data contains a text file for the room's name, which would only be used in the map. This is unusual for rooms without map data, which typically have no proper names.
- The Portal Site is the only room in the entire game that seems to be a Dark Aether version of a Splinter Hive room.
- Dark Samus Appears Part 2 is the name of the medley of themes that plays during the cutscene in this room.