Information - Awakening

When Fei and the others descended to Zeboiim, imagine their surprise when Tolone and Seraphita, along with Bishop Stone, drag out a naked green-haired little girl from a gooey tube and jet out of there. Of course, they don't know why the little girl is important or anything, and she doesn't appear in the storyline again for a long time.

During this time, Emeralda was taken to Krelian in Solaris and became a subject to observation, data collection, and possible experimentation. My guess is that since Emeralda is the product of long-lost and just recently being rediscovered nanotechnology, especially given the fact that data from the fallen Eldridge was used in her creation, Krelian wanted that technology; harming her would be the very last thing on his mind. Once she fulfilled her purpose of giving him data, he would have no qualms with letting her fall into the hands of Fei and company after her last test.

Giving her the Vierge-class gear Crescens and sending her off to the underwater reactor, Krelian's work was done. After defeating Emeralda, she became a member of your battle party, right as Solaris became accessible. Oddly enough, she seemed to recognize Fei as Kim, and while Fei tried to explain to her that he had no idea who this "Kim" was, she just jumped up and down with the repeating expression "Fei's Kim!" On the funny side, however, she fails to recognize Elly and simply calls her an old lady.

Later on, should you choose to do a side quest which involves going to the abandoned lighthouse which coincidentally is a path to another section of the ancient civilization of Zeboiim, Emeralda witnesses a few flashbacks and physically matures into a teenaged body as she realizes that Kim and Fei are not the same person.

During the ending, Emeralda's lips are silent, but a smile can be seen across her face as Fei and Elly descend to Earth in Xenogears.