What happened - a theory

See if this works... A long time ago on LV-223, something goes wrong with the WMD bottling plant in Pyramid #3. A verminous creature from an Engineer planet has stowed away and is hiding in a food storage chamber. It scurries out, runs along a tunnel, and finds some urns in the cargo hold of the attendant Juggernaut. It gnaws its way into one of them and becomes infected with goo. Before long, it is a glistening white slippery face-hugger. An Engineer brings some newly-prepared urns to the cargo hold and it's bad luck for him because he gets face-hugged and impregnated with an embryonic Deacon. Being a menial Lab Caste operative, he isn't missed for a few hours. The Deacon bursts out of his chest and wreaks havoc in the Lab facilities under Pyramid #3. It strings a bunch of Engineers up and hits them with its stinger, starting the process of turning them into eggs. The Deacon does what Xenos do best, and rounds up the rest of the crew, dragging them one by one to the eggs and pasting them to a wall. Before long, the entire pyramid and its attendant Juggernaut is infested. A squad of Deacons punch their way through doors to tunnels connecting Pyramids #4 and #2. There, they wreak havoc as before. Juggernaut #4 lifts off when an emergency escape protocol is initiated. A mass panic sets in as Engineers race to escape to Pyramid #1. Some are impregnated; others are clean; some are choking on Deacon venom spat into their breathing tubes during close combat. Meantime, the Engineers in Juggernaut #1 are in the midst of preparing their journey to Earth, and the flight data recorder is logging their preparations. A course is plot, and three Engineers retire to their hyper-sleep pods. The Pilot gets ready for flight and goes to the Energy chamber below the Bridge to make some final checks. The fleeing Engineers make their way to Pyramid #1, but for them it is too late. The scream of a Deacon is heard in the distance as they race along a tunnel when they get to the Pyramid. An alarm has been sounded, the Pilot takes action, and their way is blocked by doors that won't open. The last door to close slices the head off an infected Engineer. One of the Deacons makes its way from the Pyramid onto Juggernaut #1 and starts punching its way into the functioning hyper-sleep pods. Two of the three sleeping Engineers are stung immediately. The Pilot Engineer hears the commotion in his comms unit. He only has seconds to break open an emergency panel containing a hand-held nerve agent. He storms into the Bridge and takes on the Deacon at close quarters just as he is preparing to rip open another hyper-sleep pod. But the creature is only partially paralysed by the Engineer's weapon. The Engineer backs up as the monster pursues him. He turns to flee, pausing only to close the airlock behind him. But the Deacon is still fast, and slides through the gap despite its injuries. It follows the Engineer relentlessly. Only a short distance down the tunnel, the Engineer's path is blocked by an advancing wall of monsters. He is taken alive to be face-hugged. Time passes, and all is still, save the one remaining Engineer in the hyper-sleep pod of Juggernaut #1. The Deacons skulk off and find a discreet place to die. The eggs in the breached hyper-sleep pods lie patiently for the day when a life form leans too close. A short distance away, the Last Engineer sleeps, waiting for a time when the ship has landed at its programmed destination. Two thousand years later, he is rudely awoken from his slumber.