Check out this Radio Message from Origins.. Samantha is still trapped in Agartha and hasn't been born yet..
Ludvig Maxis: "The child's voice calls to me more frequently than ever. At first she spoke only of her imprisonment in a mythical realm known only as 'Agartha'. Now she claims to be my daughter, even though I know no such child exists! (Sigh) I fear my sanity may be slipping away from me."
Also this other Radio Message, found in Origins, explains why sometimes the Mystery Box's weapons aren't always from the same era as the one the map takes place in..
Ludvig Maxis: "When 115 is channeled towards the ancient stones, an energy field appears to drag unknown objects into purr reality. Is it possible that Element 115 is disrupting the space time continuum itself? How else could an ancient box, created eons ago bring forth weapons from different eras? Perhaps including even our own future! Further study is needed to understand these powerful and unpredictable forces."