The being known as Nephilim first appeared when Shion Uzuki encountered the Zohar Emulator that was recovered by the Woglinde. She had appeared before the scientist apparently sitting on a swing. However, before she could find out more, she was told to leave by Lt. Cmdr. Vanderkam (who was a U-TIC agent working as a double-agent in the Galaxy Federation).

The next time Nephilim was encountered was during the time the Kukai Foundation was framed by U-TIC for the destruction of the Woglinde armada (the deed was done by Gnosis). Taking advantage of an opening offered by Lapis Roman, Shion, Allen Ridgeley, Rubedo, Lt. Louis Virgil, chaos, MOMO, and Ziggy made their way to a scientist whose assistant Allen had met the previous day, the purpose being to retrieve the triple-encrypted data within KOS-MOS which would clear them of any wrongdoing. Taking a risky Encephalon dive along with Rubedo, Ziggy and MOMO, Shion encountered her again, and was taken to the tragic day she lost her parents during the Miltian Conflict. At the same time, Rubedo was forced to relive his own demons, witnessing his fellow U.R.T.V.'s going berserk because of the interference of U-DO, as well as revisiting his own experiences with Sakura Mizrahi, the daughter of Juli and Joachim Mizrahi (and the template of MOMO and the 100-series Realians).

Nephilim then revealed a startling probable future, which involved KOS-MOS in battle with U-DO near Old Miltia, which had disappeared into The Abyss. Nephilim then revealed that the destinies of Shion, Rubedo and KOS-MOS were all intertwined, and that one day, they would return to Old Miltia – and confront U-DO!

(source: Absolute Anime)