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The Lighthouse is built on the large island due north of Aquvy where Solaris is hidden. This lonely lighthouse is actually an elevator that leads down to a section of the Zeboim ruins. Down there the remaining gaps in Emeralda's history are filled in and her nanomachines suddenly react and she instantaneously matures from a little girl to a young woman in appearance.
The lighthouse can only be visited in Disc 2, after the Snowfield Hideout is explored. Because of this, the lighthouse is an optional sidequest, but a highly recommended one.