Originally intended as a sequel to James Cameron's 1986 film Aliens, the first mini-series features the characters of Rebecca "Newt" Jorden and Corporal Dwayne Hicks.

Hicks believes Newt to be the only thing that marks his existence and honors his squad's sacrifice, so he extracts her from the institution and smuggles her on board the ship flying to the homeworld.

A scientific corporation has acquired an alien queen, and begins harvesting eggs, intent on creating bio-weapons.

A weird cult that believes the Aliens to be God's spiritual rebirth breaks in and its members voluntarily give themselves up for facehugging.

Back on the ship, Newt kills Massey, but is distraught to learn that Butler, while surviving being torn in half, is one of the synthetics.

Hicks almost kills them all by waiting until he has planted the nest-destroying charges before taking off, but they receive last-minute Alien-killing assistance from a living "Space Jockey", a member of the enigmatic species who originally built and launched the derelict ship whose cargo of eggs led to humanity's first encounter with the Aliens.

Hicks and Newt receive word of the Alien invasion of Earth, but decide to return home anyway, accompanied by the Jockey in his/its own ship.

Upon arrival, they are told by a general that Earth's armed forces are abandoning the planet, planning to return once the Alien infestation has run its course and repopulate.

The Jockey remains behind in orbit; as she departs, Newt receives a final psychic warning that any returning humans will find it still there, waiting.

The story continues where Outbreak left off, with Newt, the synthetic Butler, and Hicks a short time after having escaped the alien-infested Earth on a cargo ship.

Once aboard the ship Hicks and Newt realize it is full of "trained" aliens that Spears intends on using to take back the infested Earth.

On the final page, Ellen Ripley appears, heavily armed, saying the time has come to take the battle to the xenomorphs.