David Twohy's Alien III was a script draft for a sequel to Aliens. Twohy was the third of six different writers to tackle the Alien3 project. His draft is the first that bears a resemblance to Alien3 as it was ultimately made, being set inside a huge prison/ore refinery aboard a space station orbiting Earth; this location ultimately formed the basis of the prison setting used in the final shooting script, fused with much of the plot from Vincent Ward's subsequent monastery planet story. Twohy's screenplay was written after Eric Red's script was rejected, and was followed by Vincent Ward's attempt.
Somewhere in space, a mining ship is collecting asteroids to harvest their raw materials. Suddenly the vessel's machinery shuts down in response to something detected in the rock being processed, and when the prospector in control investigates he finds a Facehugger entombed in amber amongst the debris. He collects it and sends a message to Weylan-Yutani, and the ship resumes its harvesting operations.
Three years later, several new inmates are being transferred to Moloch Island, a giant prison in orbit around Earth. The new arrivals — Styles, Grimes, Van Brundt, Domingo and Kiryu — are put straight to work in the large foundry at the center of the space station that processes ore mined in space. The giant steel ingots it forms are fired towards Earth, where they splash down in the South China Sea to be collected by ships. As they clock off that evening, a long-time inmate, Ivory, is taken away by the guards as his execution is finally due.
The new inmates struggle to find a vacant cell in the cell block, which is essentially unpoliced and run by the prisoners. A shady inmate called Bellhop offers to show them to vacant cells if they give him some of their meagre earnings from the foundry. They agree, and Bellhop takes them to the basement-like lowest level, where most of the cells are suspiciously empty, the only occupants a collection of deranged or physically handicapped individuals. That night, Styles hears strange scratching noises from the maintenance area beneath his cell.
The following morning, Ivory's execution in the gas chamber is broadcast throughout the cell block. However, unknown to the prisoners, Ivory is not killed, and reawakens inside a small bunker. Almost immediately, something begins pounding against the outside of the structure, and in moments the Xenomorph responsible breaks through and tears him apart. In the foundry later that day, Styles sabotages some of the machinery to save the lives of several prisoners, but accidentally shuts down the entire facility. One of the guards brutally attacks him for his actions, impaling him on a post.
Styles is patched up in the infirmary, the operation carried out by robotic arms controlled by a surgeon on Earth. Afterwards, Styles manges to convince the technician in charge, Packard, to give him a job as her assistant instead of in the foundry. While wary, she agrees. Styles meets some of her co-workers, including a man named Reed who works in the secretive P-4 laboratory elsewhere on Moloch Island. That night, a Xenomorph breaks through the floor of the cell next to Sykes and kills its occupant, a paraplegic prisoner, before squeezing through the cell bars and killing another inmate in the adjacent cell. By the time the guards arrive the creature is gone. The incident is passed off as an attack by a rabid prison dog.
A Weylan-Yutani representative called Mr. Lone arrives at Moloch Island to survey the progress of the Xenomorph experiments, and is shown another Xenomorph being grown in the P-4 lab. He is told it will be ready in time for the next scheduled prisoner execution. Lone makes it clear he is also aware of the attack in the cell block, and orders the Xenomorph responsible to be hunted down and destroyed. Meanwhile, in light of the attack on the prisoners, Styles and the others elect to try and escape. The following night, they make their attempt, but the Xenomorph discovers them as they move through the station's water pipes. It kills Grimes, Domingo and Kiryu, while Van Brundt is killed by a trap set for the creature by the guards. The guards kill the Xenomorph and recapture Styles, who is thrown into solitary confinement.
Styles manages to convince Packard of what has been happening, and she sneaks into the P-4 lab to investigate. Within, she finds not only the Xenomorph that is being grown, but a room containing a host of earlier attempts in suspended animation, some of which are grotesquely deformed. She also finds the tapes of the tests being conducted on supposedly executed prisoners. She confronts Lone, who convinces her nothing illegal has been done and suggests she remain quiet. However, when Packard discovers the attack on the inmates in the cells was also arranged by Lone, she decides to free Styles and escape with him.
Their attempt ends in disaster when Moloch Island's hull is ruptured by gunfire from the guards, the accident causing an incoming shuttle to crash into the station, decompressing the entire cell block and killing thousands of prisoners. The incident also causes two of the Xenomorphs being grown in the lab to awaken and escape. Styles, Packard and the few survivors with them agree they have to team up if they want to get off the station alive, which is rapidly losing air. Packard and a guard named Daggs go about making the necessary preparations for their escape, encountering the two escaped Xenomorphs fighting to the death as they do so. Meanwhile, Styles confronts Lone, who is attempting to flee aboard his personal shuttle, and throws him to his death, revealing him to be an android.
With the station's air supply finally running out and the last Xenomorph in pursuit, Styles, Packard and Daggs don space suits and leap from Moloch Island into space, hoping to reach Lone's shuttle, which is drifting nearby. They succeed and climb aboard, before flying the craft directly into the Xenomorph, tearing it apart. Some time later, the survivors are picked up by an ICC cutter.
While Twohy's setting was carried over into the filmed Alien3, forming the basis of the Fiorina 161 Class C Work Correctional Unit, none of his plot or characters were retained. However, the character of Packard bears many obvious similarities to Clemens, both being medical personnel who come to trust and work with the protagonist despite their initial misgivings. Other aspects of Twohy's screenplay later resurfaced in Alien Resurrection. Notably, the script features several characters being sucked piecemeal into space through small ruptures in Moloch Island's hull (or in one case, through the bars of a prison cell), foreshadowing the death of the Newborn in the fourth film; such a demise had originally been planned for Lambert in Alien, but had to be dropped due to the special effects limitations of the time. Similarly, the room containing glass tanks holding the dormant Xenomorph prototypes, some of which are grotesquely deformed, is very reminiscent of the "clones of Ripley" scene in Alien Resurrection.
Unlike the preceding screenplays, which generally featured increasing numbers of Xenomorphs for the protagonists to defeat, Twohy's script instead moves in the direction of the original Alien, with only a very small number of the creatures. A large portion of the story features no real contact with the Xenomorphs at all, and focusses instead on the escape attempts of Sykes and his fellow prisoners. The script also uses "Weylan-Yutani", the original name for the company in Alien.
As with all of the unproduced Alien3 scripts, Twohy alters the nature of the Xenomorphs, bestowing the creatures with fairly substantial new abilities in his story. The creatures on Moloch Island are not created through the traditional means of impregnating hosts with Chestbursters, but rather are engineered and grown by the scientists in an artificial "womb" in a lab. None of the Xenomorphs are ever seen attempting to recreate on their own, although the creature living below the cell block does begin building a Hive inside a water tank. The script also features Xenomorphs being altered through genetic experimentation, an idea first touched upon in William Gibson's script (and again later featured in Alien Resurrection, although the alterations to the creatures in that film were unintentional). Perhaps as a result of this manipulation, the creatures do not share the Hive mentality of Xenomorphs seen previously, and at one point two of the Aliens actually fight each other to the death on sight.
The genetic manipulation in the script leads to a variety of different Xenomorphs, each of which has its own unique abilities:
- Rogue Alien: The creature that is living beneath the cell block and is responsible for the deaths of the inmates in their cells, as well as Grimes, Domingo and Kiryu during the ill-fated escape attempt. This Xenomorph is able to realign its armoured exoskeleton so that it may reshape itself to pass through very narrow gaps, such as between the bars of the prison cells. The idea of a Xenomorph that can alter its body shape to pass through small gaps was later reused by Jon Spaihts' for the Beluga-Xenomorph in his original script for Prometheus, titled Alien: Engineers.
- Chameleon Alien: Only seen in the specimen storage room in the P-4 lab. This Xenomorph can change the color of its skin to match its environment as a form of camouflage.
- Brute Alien: This creature escapes from the storage room following the shuttle crash and is later killed fighting the Newbreed. It is described as stockier than a normal Xenomorph, with a spiked exoskeleton. In combat, it "charges like a mad rhino".
- Siamese Alien: Only seen in the storage room in the lab. This Xenomorph consists of two individuals fused together like Siamese twins.
- Mutated Alien: Only seen in the storage room in the lab. This Xenomorph is horribly deformed (much like the failed Ripley clones in Alien Resurrection), implied to be because of imperfections in the cloning process that created it.
- Newbreed: The primary antagonist following the death of the Rogue Alien. This creature is able to secrete acid through its skin, an ability it effectively uses to pass through walls and other obstructions by melting them. It also engages the Brute Alien in a fight and kills it by tearing out its spine. Despite its name, it bears no relation to the Newborn in Alien Resurrection.
- The manner in which the Xenomorphs are recreated from a Facehugger trapped in amber is remarkably similar to the way in which dinosaurs are recreated from a mosquito fossilized in amber in the film Jurassic Park.