Just unlocked rank 3 of the transport network. The portal doesn’t seem to exist in the little room under the ramps where it should be. I found a video online and my room is just empty. The video shows the portal to the right of the room and a swirly blue pool thing in the center. Mine is just empty. Help!
It takes some time once you buy the upgrade for it to be available. If you just purchased it, and the timer is still going, you won’t see the portal until it’s done.
If you have waited out the timer since you bought it,…then I’m guessing there is something wrong, and you’ll want to submit something over to the bug forum.
Hope that helps. 
The center of the room is the mushroom network portal. You’ve unlocked rank 3 and never used it?
If that is the case, then I suspect you never completed the initial quest that came with the first unlock. It should be in the mushroom cave in the NW corner of Ardenweald. I suspect if you never opened the mushroom network, then the portal wont appear.
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Here it is. Scroll down to the section " Opening Quest Line to Activate Fae Circles" I suspect if you do that questline everything will appear.
https://www.wowhead.com/guides/night-fae-covenant-transportation-network-marasmius
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Thank you so much!
Would suggest Blizz to add an icon on the Night Fae map for the Orbius portal. After all, there seem to be icons for everything else?
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There’s a purple icon for Marasmius’s room, isn’t there? If you navigate to that icon on your map, it’s impossible to miss the portal.