- The crew listens to the eerie signal from the planetoid.
- An additional discussion between Parker and Ripley over the comm, concerning the progress on the Nostromo's engines.
- A scene in which a furious Lambert hits Ripley for her earlier refusal to let her team back aboard the Nostromo.
- An additional conversation between Lambert and Ash, in which Lambert notices a dark patch over Kane's lungs on the scanner, foreshadowing Kane's fate.
- A discussion among the crew, immediately following Kane's death, on how to proceed further.
- Alternative death scene for Brett: Ripley and Parker witness Brett (still alive) being lifted from the ground.
- Ripley and Lambert discuss whether Ash has sex or not.
- An unfinished scene in which Parker spots the alien next to an airlock door. He asks Ripley and Lambert over the comm to open the airlock and flush the alien into space. However, the alien is warned by a siren and escapes, but not before it gets injured by a door and its blood creates a small hole, causing a short decompression.
- Ripley finds Dallas and Brett cocooned. Brett is dead and covered in maggots; Dallas is alive and begs Ripley to kill him. She does so with a flamethrower. The mercy-killing scene would eventually be recycled and used in Alien: Resurrection (1997) when an alien/human-hybrid clone of Ripley begs the real Ripley to kill her, to which she does so with a flamethrower.
Many of these scenes were included in the Director's Cut, which Ridley Scott made at the request of many fans who had seen those scenes as bonus material on the earlier Alien DVD release.
- Dallas and Parker using a craft called 'The Flying Bedstead' to enact repairs on the exterior of the ship whilst in space.
- A sex scene between Ripley and Dallas.
- The crew using internal cameras to look for the alien where they find it halfway matured looking something like a cross between the chest-burster and an egg with feet.
- Dallas' death was to take place in a huge upside down 'wind tunnel' in the air duct system. Dallas looks up to see the alien on the ceiling of this massive cylinder, where it leaps from one side to the other in a super-fast descent toward him.
- The alien was to pull Ripley out of the shuttle with the grapple wire where she shoots it with a pistol and makes her way back inside before destroying it with the engines.