Deleted Scenes
The script for this film had a lot of potential. Most of which can be seen here in the deleted scenes. Some of these have been reinstated in the Alien Quadrilogy's extended version of the movie. Nearly 30 minutes of footage was cut from the theatrical release. This list is in chronological order.
File 01: Dark Dream
A black-haired woman stands with a young black-haired girl in an enormous wheat field. A girl's voice says, "My mom always said there were no monsters, no real ones, but there are." The girl looks up at the woman, but she is already more than fifty yards away. The child slaps at a bug on the back of her neck. She pulls it off. It's huge. The sound of insects fills the air. The strange bugs swarm the little girl. There's a rising sea of blood. The child opens her mouth to scream, but the black insects race down her throat. Ripley 8's dream ends.
File 02: Awakening

Wren tells Gediman and a surgeon to sew Ripley 8 back up while the other scientists remove the Queen Chestburster from her. Gediman says, "Well, that went as well as could be expected." Ripley 8 wakes up. She grabs the surgeon's forearm. He yells in pain. Her fingers dig into his skin. The other people scramble, knocking things over. The surgeon's bone cracks. Ripley is sedated.

File 03: Hell's Garden

After Call interfaces with the Auriga's computer to stop Wren, the survivors up to this point enter a sector of the ship filled with a colossal garden. This supplies most of the food for the Auriga's crew. St Just, a main character in the script who was merged with Christie in later drafts, finds a platform jeep. They all get on it. Ripley 8 drives it through the immense jungle. An Alien leaps out of the vegetation onto Hillard (she survives the water scene in the original script). The Alien's tongue punches a hole in her head. St Just kills it. Ripley 8 floors the jeep.

More Aliens emerge from the brush. One jumps down in the vehicle's path. Ripley swerves the jeep off the road into the foliage. Johner almost falls off, but Vriess saves him. St Just gets wounded in his gut by an Alien before blasting it. The jeep bounces down the slopes of the garden, rocking violently with the Aliens close behind. It veers into the left hall at the end of the garden. Ripley 8 brings it to a stop.

Everyone piles out, shooting at the creatures all around them. The Aliens' acidic blood starts to eat through the hull. St Just can barely walk. The others urge him to move. "You go," he replies, "I'm bored." He pops some pills into his mouth, grinning slightly. Wrist guns in his palms. Everybody else runs, trying to get out of the sector before it depressurizes.

St Just stands his ground, firing at the swarm of Aliens. Their bodies pile up. More acid melts the floor. He runs out of ammo, pulling out two more disposable wrist guns. He continues to blow away the enraged beasts. His face is cool and steady. His guns' click empty. "Damn," he says. The hull bursts open, pulling everything in the garden out into space. The others make it into another sealed sector just in time.

This would've been an amazing scene, but sadly, I don't think it was filmed. The still above comes from a magazine on the production, and it suggests there may have been some footage of this, but it seems unlikely given the way everything else in the film plays out ie there's no St Just, Christie dies in another scene, Hillard drowns, etc.

File 04: Waste Tank 5
In Waste Tank 5, the location of the Queen's nest, Ripley 8 originally hangs upside down from the ceiling. Gediman hangs next to her. He tells her that the Aliens have been draining him. Blood drips from wounds on his feet into a pool on the floor. The Queen is killed by the birth of the Newborn, which is described as a spider-like creature with no eyes. It has pincers on the sides of its mouth, and red veins running through its body. The Newborn spots a soldier hanging from the ceiling. He begins to scream. It leaps onto him, inserting its tongue down the soldier's throat to drain his blood. Its pincers hold him in place. After the Newborn finishes, it kills Gediman next.

Ripley 8 escapes from her resin cocoon, falling into the pool just as the Newborn jumps at her. She emerges from the black water with a rifle the soldier had, shooting several nearby Aliens. She spots light coming from some holes she shot in the tank. She breaks out of there. The Newborn struggles after her, but it's too big. Ripley escapes through a vertical shaft.

File 05: Alternate Ending
Call and Vriess pilot the Betty out of the Auriga's airlock while Ripley 8 and the Newborn hold onto the outside of the ship. The Auriga crashes into snow-covered mountains. A wave of fire chases the Betty. Johner sees Ripley holding on but refuses to open the hatch because of the Newborn. The shockwave from the Auriga's destruction shakes the Betty. Ripley 8 is thrown off, but she grabs hold of one of the Newborn's tentacles. Call pushes Johner aside, opening the hatch. The Newborn heads straight toward it, but Call comes out with a Grenade Launcher, blasting it. It merely wounds the creature so Call fires again but misses. Ripley 8 climbs inside. Call seals the hatch as the Newborn rams into it. She takes over piloting beside Vriess as the Betty nears the wooded ground below. Johner informs the others the Newborn is behind the thrusters, avoiding debris. Call turns the engines on, burning the creature.

The Betty crash lands. Call checks to see if the Newborn is dead. Its flesh is black in spots, but in other places, new pink flesh is visible. It lunges at her, shooting its tongue out. Call dodges it, barely avoiding it at the last second. The Newborn runs away. Call grabs the Grenade Launcher to go after it, but Ripley 8 convinces Call that she should go instead.

Ripley hunts the Newborn by following its tracks in the snow. She races through the trees, reaching a cliff face where she sees a huge city in the distance. In the darkness, the Newborn rises in front of her. It hits her with its tentacles. Ripley manages to get a shot off, but the creature is only stunned. It knocks the futile weapon away.

Call comes to the rescue in the Harvester, ramming it into the Alien and knocking it down. The Newborn gets back up only to be hit by the Harvester again. Its tentacles shoot out, hitting Ripley 8 off the cliff. She manages to grab hold with her nails digging into the edge. She starts to crawl back up. The Newborn throws the Harvester off it, but the vehicle charges back at top speed, crashing into the creature. The Harvester is thrown upside down from the collision.

Ripley 8 reaches the top of the cliff, racing for the Grenade Launcher. The Newborn flies at her, but she fires and fires, knocking it back until the gun runs out of ammo. Ripley 8 screams and lunges into the beast, sending them into the Harvester. Call throws a lever activating the machine's blades. They shred the Newborn. Ripley gets free from the Alien's grasp. She helps Call escape from the Harvester as acidic blood rains down. The vehicle explodes. Call, Ripley, Vriess, Christie, and Johner gather around the fire, relaxing. They decide to leave before troopers arrive.

Some of this ending appears to have been filmed, because there were early test screening reports about the Harvester.

The extended cut on the Quadrilogy ends with the Betty landing in France near the Eiffel Tower.