I have been thinking about that myself. What I am coming up with is that the Doctor spent what, 20 something years in the box? Seems to me since he worked on it that he was testing it for a bigger purpose. I believe this all lead's back to Rambaldi since the box was designed by Mueller and Mueller is linked back to Rambaldi...I'm thinking that they are going to try to put Sydney in the box after the baby is born. I thought maybe they would want the baby in the box...but Irena thinks that Sydney is the "chosen one"...so I wouldn't be surprised if they were doing this because of some Rambaldi prophecy.