This is the end of the first attempt to bring the Emperor through. There will be more. Look at the Commune Morningstar cast a few runs ago. The divine answer was pretty clear about this trick working "this time"
I think the Company's next task, after training, and a flurry of magic item creation (Ernie needs a Fly item SO badly), will be to go to Kivia, recover the third Eye of Morel, and go Nowhere. From there, we suspect we can use the Focus, the Maze, the Opener, the Light and the Eyes to disconnect the connection between the two planes, finally removing the weak points between the worlds. The archmagi can then retire to a beach somewhere (all except the one in the Mouth of Nahalm, who's probably had enough sand).
Then we just have to deal with Parthol, who wants the Spire dead with or without the Emperor, that wierd Slayer prophecy, Shreen the Fair, destroy the Guild of Chains, Save the halflings of Appleseed and...
Did I get everything?