The film begins with a promise from Burke to Ripley that they are going to destroy the aliens, not try to save eggs to study. And it ends with that promise broken when Burke locks Ripley and Newt into their room with a face hugger. While the aliens are incredibly dangerous to every single person on the mission, the story reveals how fallible human beings are to the destruction of their morality which violates the rights of others. There are two enemies, the outward (aliens) and the inward (certain members of the crew, and ones own fears).
In the end, it is Bishop an artificially intelligent android that saves the crew. It is his knowledge of the colony and his willingness to risk his life tunneling through to the nuclear reactor that allows the crew to even have a chance. Couple that with Ripley's unwillingness to allow harm to come to Newt and we see the blending of technology and humanity used to save the remaining crew. This film is a statement about power. Burke represents those who will do anything to grow it even at the risk of killing everyone on the earth by bringing eggs back. And Ripley represents those who will stand in opposition to every threat against our humanity. Burke mobilizes a Marine force which is meant to protect in order to essentially endanger humanity. The film reveals how those in power manipulate the forces at their disposal for their own personal gain.
And that is the grave danger the crew must defend against while simultaneously having to killing the alien lifeforms that are attempting to kill them as well. The external assault is only enhanced when the added assault from within comes as well. It is only by the willingness of sacrifice (Ripley, Hicks, Bishop) that anyone is able to escape.
