The Portal Site is entirely identical in architecture to the Portal Terminal, its Light Aether counterpart. In a cutscene, Samus jumps through the Light Portal that would take her back to Aether, and then walks towards the end of her Safe Zone, to see how hazardous Dark Aether's atmosphere is by putting her left hand through; she immediately pulls it back in, as the atmosphere slightly burns her.
A tutorial message then appears onscreen: "Dark Aether's atmosphere is dangerous. Glowing Safe Zones protect you from Dark Aether's atmosphere. Some Safe Zones must be shot to function. Shoot the sparkling energy nearby to energize the Safe Zone. Energized Safe Zones don't last forever! To reactivate a Safe Zone, shoot the sparkling energy again." Bladepods, Light Portals and Light Crystals and Light Beacons can first be scanned here.
Samus' main goal in the Portal Site is to activate a Bomb Slot in a state of transdimensional flux. This action lifts a gate blocking the door to the Transport Center. On subsequent visits after defeating Amorbis, three Dark Pirate Troopers try to ambush Samus as she escapes the room, although if she has the Light Beam, she can turn the tides on them by luring them into a Safe Zone, and then she can supercharge it to incinerate them.
- 3 Dark Pirate Troopers (after Amorbis fight)
- "Morphology: Dark Pirate Trooper
Darkling-possessed Space Pirate.
Enhanced strength and stamina gained from addition of symbiote. Dislikes bright light."
- Portal generation system
- "System analysis complete.
Console used to energize and open a portal to Aether, currently online.
Portal generation system initiated."
- "Morphology: Bladepod
Living storage units of the Ing Horde.
These Ing morph their bodies around useful items to protect them. They rely on larger Ing for protection."
- Light Crystal
- "Xenotech: Luminoth Light Crystal
Generates protective field of light energy.
Light Crystals provide protection from Dark Aether's atmosphere. They can be nullified by dark energy and supercharged by light energy."
- Light Beacon
- "Xenotech: Luminoth Light Beacon
Generates protective field when energized.
Light Beacons must be energized by Beam weapon fire to function, and remain charged for a limited time."
- Bomb Slot
- "Device: Bomb Slot
Powered system control unit.
Insert the Morph Ball into the slot then detonate a Bomb.
This will transfer energy from the slot to the device connected to it."
- In the Trilogy version of the game when the Dark Pirate Troopers attack Samus in this room, the Space Pirates theme plays until she escapes the room or kills all of them. This music does not play in the original Nintendo GameCube version.
- While the Space Jump is meant to be acquired in order to return up the platform to access the portal, Samus is able to jump onto the Luminoth Light Crystal and reach the upper level without it.