Board Thread:General Discussion/@comment-4913740-20130707123202/@comment-82.123.253.68-20130707175153

Mr. Grave wrote: 82.123.253.68 wrote: With the Phantom Pain, we can add Skull Face, Quiet, Code Talker and many others to come to your list. It's not known yet if Quiet, Skull Face, Code Talker are new characters. I hope so.

So, for the moment, the main theory is that Quiet is The End's grand-daughter.