Ripley, Jonah, Vriess and Call have landed on Earth to discover it has been overrun by the Xenomorph and destroyed by nuclear explosions in a last ditch attempt to wipe out the infestation. This turns out to be the reason why the Corporation wanted to study the creature; to try to control it after having unleashed its kind on Earth.
With no fuel to fly and nowhere else to go, Ripley and co head deep underground in search of safety. Here is where they discover that the source of the infestation came from a previous clone of an impregnated human... Newt!
Cloned from a sample of her DNA, the same as Ripley, as now also of the late Bugstomper, Corporal Dwayne Hicks, she has been reborn a hybrid of the two species and is being used by the surviving employees of Yutani-Weyland to try to control the hives. Corporal Hicks, now a Lieutenant leading the clones of hardened veteran soldiers against the hive, doubles as Newt's father figure; a very realistic reason why Newt won't unleash the Alein on the bastards using her against her own will.
United again unwittingly, having no clear understanding of who they once were, the former allies join forces once more, in the event of escaping a nuclear core meltdown at the Weyland-Yutani complex, not only to survive the Alien but to destroy the Corporation and their many times recloned leaders once and for all before they cause humanity's outright destruction!