In End of the Circle, the SDF-3 is sucked into some weird alternate dimension. These "shadows" (in the book they are glowing orbs of light) abduct Valkyries and their pilots. Then, the kids on the SDF-3 start chanting for some reason... I can't even remember why. I think that the SDF-3s protoculture drives were taken from the ship. The Haydonites back in realspace are stirring up trouble and Tirol is transforming (wtf?) and going to some blackhole or something.
Then, Minmay and Zor Prime (or one of the Zor guys) are on some planet in this alternate dimension where they find the SDF-1s protoculture drives and theres these little bunny things running around.
So somehow, the SDF-3 gets back to Earth and it is happily ever after. I imagine that TSC will cover the ship's journey back home in this alternate dimension thing.
I just re-read that thing this spring and that is all that sticks out to me. As you can tell, it sucked.