In October 2012, the Prometheus Blu-Ray set was released which contained 14 deleted scenes. Here’s a handy guide to all the Prometheus Deleted Scenes.
Arrival Of The Engineers [2:31]
This is an alternative opening which shows an Elder Engineer handing the Sacrifice Engineer the dark liquid. Several other Engineers can be seen standing in the background. There is some slightly different editing and the sequence showing the Engineer disintegrating is slightly longer. When he falls into the water, the sequence where the cells are dividing is slightly longer. This deleted scene was changed because they wanted to keep the Engineers more mysterious.
T’is The Season [0:58]
The scene shows Vickers walking into a room where Janek is decorating a Christmas tree. She tells him that the mission briefing is about to start but Janek doesn’t really care why they are there.
Our First Alien [0:42]
This scene is one of the few scenes that would have been beneficial to keep in the film. It explains why Milburn was so fascinated by the Hammerpede creatures later in the movie. In this scene, he basically discovers an indigenous worm in some black liquid. He’s enthusiastic about it as they’ve never discovered any other life larger than bacteria before. This scene also makes it clear that the worms are indigenous creatures to that planet and the dark liquid is responsible for mutating them.
This scene picks up with Milburn and Fifield in a tunnel after they left the other group. They discover some skin on the ground which Milburn picks up. Presumably this is the skin from the Hammerpede creatures.
We’re Not Alone Anymore [1:22]
Shaw is telling the Prometheus crew a story about how the world came to be. She says she has spent her whole life looking for what they have found today and that they aren’t alone anymore. What follows is some remarks from Holloway who says he isn’t happy that all the creatures are dead.
Strange Bedfellows [2:57]
The scene shows Shaw in her room watching a video of the Engineers that were seen in the holograms. Holloway then enters her room who is really drunk. They talk about the video and theorize what might have happened to the creatures. What they were running away from in the first place. Then Shaw mentions the head they just inspected and why it might have exploded. Holloway is still upset because he was hoping to find more on the planet. Holloway then asks why Shaw came here. He remarks that she came here to ask God why they took her mother and father, and Shaw slaps him. She tries to run but Holloway grabs her. She’s still struggling and then they start kissing and are about to have sex.
Holloway Hungover [1:25]
The scene where Holloway discovers something in his eye is slightly extended in this deleted scene. After speaking to Janek over the radio, Shaw goes over to Holloway and asks him if he is okay. Holloway says he thinks he is hungover.
David’s Objective [0:23]
David is exploring in the one of the tunnels which Vickers is on the Prometheus ship. She tells David over the radio to get back to the ship. She asks him if he has located his objective. David says he has and it’s now time.
Janek Fills Vickers In [3:27]
The scene takes place after Vickers kills Holloway. Vickers is sitting in her room when Janek visits her. He tells her a story about when he was in the military and a particular mission he was part of. David then interrupts over the radio and tells Janek about some seismic activity below ground. David asks Vickers if ‘he is awake’ referring to Peter Weyland.
A King Has His Reign [3:40]
This sequence has some additional dialogue and editing. This scene shows David and Ford helping Peter Weyland into his spacesuit when Vickers enters. Weyland remarks that the last time they spoke, she said he was nothing but a silly old fool chasing fairytales. Vickers tells him that she is sorry and she came to say goodbye because he’ll die if he goes down there. Vickers says that a king has his reign and then he dies. She tells him she used to respect him, looked up to him but now he’s nothing but a scared old man. I guess this scene further shows the turbulent relationship between father and daughter.
Fifield Attacks [2:01]
This sequence shows Fifield attacking the crew at the hanger bay like in the movie. The scene is exactly the same frame by frame, apart from the design/CGI of Fifield, which is completely different. He appears to be more alien-like, and could possibly be transforming into a xenomorph. I must admit I do prefer this design as I was never a fan of the mutant-like creature we got in the movie.
The Engineer Speaks [4:06]
The conversation between David and the Engineer has been greatly expanded in this deleted scene. David first tells the Engineer, at Weyland’s request, they came just like they asked. The Engineer gets out of the stasis tube and stumbles forward. The Engineer asks, in his own language, why they came. Shaw interrupts like in the theatrical version. Weyland tells David to tell him why he came. David tells the Engineer that Weyland wanted to live forever and the Engineer asked why. Weyland tells the Engineer that his company made David from nothing. He says that him and the Engineer are superior, that they are creators, and gods and that gods never die. The scene carries on as in the theatrical version where the Engineer kills everybody while Shaw escapes. There is some different sound effects in the scene. You can hear David say sorry when his decapitated head hits the floor for instance.
Final Battle [5:30]
The scene takes place when Shaw climbs into the lifeboat. She wanders into the room and sees young Shaw playing the violin as in the theatrical version. The scene is a bit longer though. She has a drink and injects herself with some more medicine. She goes to the Medbay door and sees the creature as in the theatrical version. She then hides in the other room behind a counter. The Engineer soon enters the room and watches the video of a young girl playing the violin. David then interrupts over the radio which reveals Shaw’s presence to the Engineer. She hits him with an axe a couple of times before he grabs her by the throat. He throws her against a wall and he walks towards her. She hits him again with the axe, this time in his leg, he grabs her again and she hits him in his torso. She runs off leaving the axe embedded in his body. He catches up with her, throwing her into a wall again and picks her up with both of his hands gripped around her head. She opens the Medbay door and the scene carries on as in the theatrical version. Note that some of the effects are unfinished in the deleted scene. For example, the Engineer’s face isn’t burnt on one side like in the finished scene.
This scene takes place at the very end of the film. There is some additional dialogue between Shaw and David. Shaw asks what the Engineer said to him and where he came from. David said there is no direct translation but several cultures had a word similar to it. That word was Paradise. When the camera pans out to show Shaw in the vehicle, note that the CGI Juggernaut ship is not in the deleted scene. When Shaw gets to David in the ship, Shaw says some extra dialogue. When she’s talking about where she wants to go, she says she wants to go to Paradise. The next dialogue is actually said in the theatrical version but she says it when she’s about to descend out of the ship. David asks her what she hopes to achieve by going there. Shaw says they created us, then they tried to kills us and then they changed their minds. She wants to know why. David questions why she wants to do this and says he doesn’t understand. Shaw says that’s because she’s a human being and David is ‘a fucking robot’. She picks up David’s head and shoves it into a bag. The scene definitely paints a different picture of Shaw here. In the movie, she was apologetic for putting David’s head in a bag.