When Call and Wren reach the top of the shaft first, Wren talks her into giving him her gun and shoots her in the chest.
Her body falls back down into the water and drifts away. Ripley is horrified, as she has found something strangely compelling about Call. Wren escapes the shaft and seals everyone else inside, but the door eventually opens again from the other side. Call has somehow survived the gunshot and rescued them. Ripley is not fooled, as she knows she saw Call get shot in the chest at close range.
She makes Call show everyone the wound, revealing wires and white android blood. Call confesses that she is one of a legendary model of androids who were so lifelike that they gained consciousness and rebelled, burning their internal wireless modems and trying to pass themselves as human. The soldier Distephano (Raymond Cruz) who is with them is geeked about actually seeing this kind of android.
Call seems humiliated that her secret has been discovered. Ripley now understands why she feels a kinship with Call; both of them are somehow artificial, creatures that have been created in the likeness of human beings but who are distinctively different.
Call reveals that before she burned her modem, she accessed the mainframe and discovered the plans that General Perez had for cultivating the aliens by cloning Ripley. Her personal mission was to destroy the operation and keep this from happening, as she understands that the aliens will wipe out humankind. Knowing Call's capabilities, Ripley takes her to a small chapel, where they find a computer interface.
Although Call does not want to make use of her android functions, Ripley urges her to take over the Auriga's computer. Call discovers that the Auriga went into emergency mode after the attack.
It is now automatically returning to Earth, where surely the aliens will escape and infect the human race. Ripley instructs Call to crash the ship in any way possible. Call blocks Wren from reaching the Betty and makes a sarcastic page summoning all aliens to the deck where he is.
When they set out for the Betty again, Ripley is snatched through the floor grating by aliens. Her connection to the creatures comes full circle; they recognize her as one of their own and take her to the nest, which is crawling with aliens and which also contains the queen.
Gediman is there as well, cocooned and delirious, and he tells Ripley that the queen inherited Ripley's human reproductive cycle.
After laying her first round of eggs, the queen gives birth as a human being would, developing a strange, uterus-like pod.
The queen gives birth to a bizarre creature that resembles a human being crossed with an alien.
This "Newborn" kills the queen and embraces Ripley as its mother.
It attacks Gediman, biting off the top of his head. Ripley escapes the nest and races to rejoin the others as the Betty takes off. She makes it just in time, making an impossibly long leap from the deck to the ship. With their pilots dead, Ripley seems to be the only one of them who has the experience to fly the ship. "Are you kidding?" she tells them, "This piece of shit's older than I am." There is final confrontation when Call goes to close the bay door and discovers the Newborn has stowed away. She barely manages to evade it. Distephano comes into the bay and is killed.
Ripley senses that something is wrong and comes back to find the Newborn cornering Call.
She distracts it by speaking soothingly to it; it trusts Ripley as it thinks she is its mother. She deliberately cuts her hand on its sharp teeth and flicks her acidic blood onto a glass porthole.
Her blood dissolves a hole in the glass, depressurizing the cabin and sucking the Newborn onto the window. It hovers there pitifully as it is slowly drawn violently out through the tiny hole.
Ripley feels torn between her desire to exterminate the species and the loyalty she feels toward them since she has their DNA. She watches in horror as the Newborn is slowly destroyed, aware that it is dying.
The Auriga crashes on Earth and is destroyed.
The Betty breaches Earth's atmosphere safely and Ripley and Call look out the porthole at the clouds and the sun.
They are dazed by their experience and wondering what the future will hold for both of them. Neither one has ever been to Earth before.
In the alternate version of the film released on DVD in 2003, a wide shot shows Call and Ripley sitting in the hills overlooking a desolate and ruined Paris.