My rewrite for Prometheus plays on Mike's observation that the movie should be about how humans want to know what their origin is but the answer is horrifying. This is echoed and underscored by David's own journey of horrifying discovery.

I mostly have problems with the first part of the film, where the characters have no command structure and constantly do stupid things. But I changed more of the second half because couldn't leave the engineer in. That character just makes no sense.

BACK STORY
(This doesn't need to be the opening; David reveals it later.)
1. An engineer seeds human life on earth by hybridizing engineer and ape DNA (his ancestors seeded the original life on earth and watched it evolve). He releases a number of proto-humans into the wild. 2. Other engineers watch the experiment for a long while and decide that the human experiment is a failure and intend to shut it down. 3. But the biological weapon they create for the purpose (Giger's xenomorph, appearing here as a worm initially) gets out of hand, crashing their ship far from earth.

PROLOG
Shaw and Holloway discover intelligent life on LV-223 via probes targeted at planets exhibiting SETI anomalies. Weyland agrees to fund an exploratory mission. This could be the biggest scientific discovery in history.

ACT 1
David, who is noticeably a robot, wakes the crew of the Prometheus, but with a little added eccentricity that shows David toying with free will.

Vickers is the mission commander; Janek the captain; Shaw and Holloway the exploratory team leads. Shaw and Holloway picked their own team. Everyone knows everyone else and is prepared to search for evidence of intelligent life. The briefing starts with a video pep talk from Weyland before the bridge crew explains what it found in the initial survey: a non-natural structure.

(20 minutes, just like the film)

ACT 2
The field team explores the structure which turns out to be the engineers' ship, which should be a bit more spaceship-like. They find a decapitated engineer without activating the hologram recording.

A storm is coming, and the explorers rush samples back to the Prometheus, purposely leaving Millburn and Fifield to set up an inflatable field lab inside the engineers’ ship (then they can take off their helmets). This Fifield is a technician and not a geologist. The rest of the team barely make it back to the ship before the storm hits; altho David saves them, he shows a hesitating concern for his own safety that is noticed by Vickers.

In the field lab, biologist Millburn examines the head and is astonished to find a human-like face under the helmet. Millburn is killed by the worm xenomorphs while comms are down. Trapped, Fifield is infected by the squid version that gestated in Millburn. He relays garbled video that only David can piece together and which he keeps to himself.

Intercut with that, Shaw and Holloway examine devices brought back from the engineers' ship and are able to make a little sense out of them. Holloway triggers a hologram that allows him to explain back story 1: the origin of humanity. They show this to Vickers (with David). David relates it to the way Weyland Corporation infused his mechanical structure with sentience, which disturbs Vickers.

Vickers and David record a communication to Weyland, who is still on earth. David warns that something in the engineers’ ship killed them. He further muses that humans now know their maker just as he knows his. Vickers dismisses David and tells her father that David has become "eccentric".

Vickers asks the bridge crew to send the message as soon as the weather clears. She warns Janek about David and, when taunted about her about her own robotic behavior, sleeps with Janek. After all, everyone is in a celebratory mood: they have found incredible scientific discoveries, and only David knows the full story about the field lab.

Later, Weyland’s reply arrives. He is thrilled with the discoveries but says that David must be reset and notes that future versions must have less potential for autonomy; his language suggests that David is a failed experiment. David eavesdrops and is horrified.

Holloway and Shaw discuss the fact that humans were engineered by an alien race. In this version, this is a surprise, not the purpose of their mission. They find it disturbing but scientifically thrilling.

Out of envy and a desire to wreck the mission, David deliberately infects Holloway with a tiny worm he finds among the material they brought back. “If a massive dose worked so quickly on Dr. Millburn, what would a tiny dose do, I wonder?”

(60 minutes - halfway thru the movie)

Holloway and Shaw sleep together.

The field team returns to the engineers’ ship and finds the ruined field lab, dead Millburn, and a disturbing organic cargo. Holloway, heretofore unaware, begins displaying symptoms Millburn displayed. Holloway is taken back to the ship but refused entry. Holloway takes off his helmet; a squid xenomorph bursts out and is fried.

Intercut with that, David finds the engineers' control room and activates a ship’s log hologram that allows him to learn how to operate the ship. Instead of finding a living engineer, David is able to activate a hologram representation.

Shaw discovers (with the Scottish woman Ford, rather than David) that she has been impregnated by the xenomorph via Holloway. The two go to the med-pod (which in this is for anyone; Weyland isn't on the ship), and Shaw gets the squid xenomorph extracted, but it escapes being dumped into a bio-waste bin.

Shaw remains in the pod for 8 hours while the machine performs special rapid healing. During that time, David works with the engineers’ computer and teaches it English. From it, he learns back story 2: the ship’s mission to destroy humanity. He is gleeful.

As David returns to the ship, squid-zombie-Fifield appears and infects three other crew members with the next version before it is killed.

When Shaw awakens, Ford is there. Her mouth opens to reveal a xenomorph extensible jaw. The squid xenomorph has hollowed out the back of Ford’s head. Shaw escapes and traps it in the room.

Shaw and Janek agree that they need to leave the planet. David explains that since he activated the ship, it can now be found by other engineers, who may complete the original mission and destroy humanity. In a huge step for him and a huge shock for the humans, he refuses to go and shut it down alone. “I want you to go. It’s ready to tell you anything you want to know. Don’t you want to meet your maker?”

(90 minutes)

ACT 3
At David’s urging/taunting, Vickers demands that a team go back to the engineers’ ship and retrieve more artifacts and then shut down the ship. She leads a team into the ship, including Shaw and Janek.

David eagerly demonstrates the controls and introduces them to the hologram representative. He uses it to explain back stories 1, 2, and 3, even showing holographic images of the engineers being killed by the escaped xenomorphs. The computer explains that there are other ships like this one, other experiments on other planets, and other forms the xenomorph can take. David mocks the humans as failed experiments.

Then three 3rd gen xenomorphs enter, closer to the classic version, with acid blood. They followed from the Prometheus, where they had gestated after Fifield infected others. They attack the team except for David, who has no DNA, which he finds amusing.

The humans fight the xenomorphs. Two are killed relatively easily, altho the acid blood of the first kills the remaining mercenary. The third kills Janek and carries off Vickers, which David finds distressing.

Then the ship’s engines ignite. The hologram explains that the engineers have activated the ship remotely and are summoning it home. It will be kept in quarantine until it can be cleaned and examined. David regrets his actions and helps Shaw use the xenomorph’s acid blood to destroy the controls, wrecking the ship as it lifts. They barely escape with a jet pack or some bullshit, but Shaw’s helmet is cracked. David takes his off and gives it to her.

David carries Shaw back to the Prometheus, racing ahead of the third xenomorph. He says he wants her to survive so that humanity will understand how insignificant it is. They kill the xenomorph in the loading bay with the flamethrower. The two remaining crewmen prepare for launch.

Shaw asks David to take her to the med-pod, where she tricks him and locks him in with the 3rd gen xenomorph that gestated in Ford and which wants to kill him. Shaw tells him “This one isn’t so smart.* It doesn’t know that you’re not human. I guess it’s a failed experiment.” David hides in the pod itself, but Shaw activates it, and it disembowels him. (A machine designed to help instead kills, just like David himself.)

EPILOG
Shaw returns to the bridge and gives her warning narration and ends with “Who knows what else is out there? What other forms this xenomorph can take?” Meanwhile, we see three familiar-looking egg pods in a corner of the ship’s bay.

* It was gestated in Ford by the gen2 squid that Shaw extracted prematurely, so it is imperfect