Alien3, Ripley's Queen Xenomorph

Okay, just a quick question as it's been bugging me for a while and I haven't seemed to find anything about it on the internet. In Alien3, the way I perceived it was that Ripley finds an alien on her scan, and that it is in her head? At least that's what it looked like to me when watching the film. If this is the case then, in the theatrical release, why does the Alien then come out of her abdomen at the end? I'm probably just missing something and the answer will be obvious.