Developing inside the host, this stage of the lifecycle is refereed to as the embryo or spore stage. This begins before the facehugger has actually departed from the host. Immediately after the embryo has reached the body cavity suitable for gestation (from the transplanting of the facehugger's long tube), it begins to feed off of the host. Using the host's fluid and resources, the embryo grows and develops. This can take a period of anywhere from a few hours (as with Kane in 'Alien') or a few days (as with Ripley in 'Alien3'). Even though the chest bursters that came out of them were both the same size, why the time difference? Taking into account the parallels between the aliens and an insect colony, two Alien hives will be in competition if they are close to each other. Therefore the incubation period of queens is higher to enable the unsuspecting host to move further from the original hive.

There are beliefs that during this period, the embryo consults the host's DNA as to the best way of developing. According to this belief, the embryo would take on traits of the host and therefore become most suitable developed for the environment that it will live in after it has left the host. Supporting this belief is the fact that the alien in 'Alien3' ran around on all fours, very quickly. The embryo had developed inside of a dog, and the adult alien seemed to have many dog-like traits. According to Ripley it was different than any she had seen before. This theory is not totally supported due to the facts that the egg seen at the beginning of 'Alien3' was different, and the original script had the alien developing inside of a cow, not a dog. After filming of the movie involving the alien was complete, it was then changed into a dog.