Here's my timeline of the alien story following Tiers 1-3 mentioned here:
As a franchise consultant to 20th Century Fox on ALIEN, Predator, and Planet of the Apes, I often had to take a long hard look at a number of long-beloved franchise stories and try to figure out ho…
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but with discrepancies resolved. Also, not all works are mentioned because several don't create discrepancies (I think):
The prequels take place.
New media explain how Weyland-Yutani (W-Y) fails to receive or loses all information about the aliens encountered in the prequels. All they know is that there are aliens and ships. They also set up a bio-weapons division and special orders to monetize any finds. Works like David's drawings are discovered only much later.
They detect a signal from LV-426 and think it might be one of the alien craft. When the Nostromo is docked, they have the science officer replaced with Ash and prepare to have the ship investigate the signal.
When Nostromo is closest to LV-426, Mother detects the signal, wakes up the crew, re-routes the ship based on company instructions (and thus overriding any orders from Dallas, the Nostromo captain), and has the signal decoded partially what little info the company got from the events in the prequels. It's not a distress signal but a warning.
The first movie takes place.
Create new media explaining how W-Y fails to receive or loses all information from Mother, including the coordinates that give the location of the signal.
In the Isolation game, one ship recovers the Nostromo flight recorder and visits the derelict ship. They deactivate the beacon, The rest of the game follows.
Create new media explaining how W-Y loses all information about what happened in the game such that they have to wait to get the coordinates from Ripley's lifeboat flight recorder.
Ripley is rescued by a ship working with others and doing mining on a rock, where they encounter aliens as well. Ripley's memory of the encounter is wiped off, and she is left in cryo-sleep and drifting in space once more.
Create new media explaining how W-Y fails to receive or loses all information about what happened to Ripley in that adventure.
Media explaining what happened to the colony and the second movie takes place. Create new media explaining how W-Y removes the coordinates from the flight recorder to explain why the board does not want to heed Ripley's request and investigate the Nostromo landing site.
Create new media explaining why W-Y sent only one squad of Marines and a warship with no captain and crew. It can point out that the company believed that only two aliens were involved, which is why it sent only one squad. Also, W-Y and certain military officials were colluding and working covertly against the ICC and ECA, which is why it sent a ship that was about to be decommissioned on automatic pilot, and a Marine squad that was supposed to be demobilized.
The rest of the second movie follows.
Create new media showing how the colony is destroyed but the derelict ship is not damaged. Various ships revisit it following the W-Y Report and ACM Manual, but those and the derelict ship are destroyed by volcanic activity caused by the explosion from the colony. This explains why, without anything from the derelict ship, W-Y needs to get the alien and embryo from the prison.
The third movie follows.
Great minds and all that! 
