Here's a recap from WAY back and how it applies to now.

The 1: The engineers  in the first scene of prometheus and the engineers the prometheus crew meets have several important differences. I'll skip deleted scene stuff since that isn't always canon but we will call the first engineers Elders from here on. Elder wasn't wearing biomechanics suit. Elders had different ships Elder's actions foster new life on earth, and cave paintings interactions recorded do not appear malevolent. Given the engineer's reaction after cryosleep, it would follow that the attitude toward our race has changed or the engineer is not of the same ideology as the Elders.

2: Pointing us toward LV-223 being a trap is completely illogical. If they wanted to innoculate our planet with black goo, they could send a ship to us. That was clearly where the plan had gone.  It appears there was an ideological schism amongst the engineer's and the Elders. 

3: 2000ish years prior to the prometheus is probably when the schism occurred. It is not unreasonable to say that LV-223 was a welcome planet until the Engineers stole or developed the black goo and took over the planet to mass produce it and use it as a staging point to eradicate all of the Elders seed planets. 

4: Aliens Colonial Marines was an obnoxious, train wreck, charlie foxtrot, abomination of a video game, but it was allegedly canonical story wise. There was an easter egg  that depicts a space battle. This is the video that involves a juggernaut and a round ship which the juggernaut loses.

5. LV-223 is in the same system as LV-426 and David was instructed to investigate the message that was ALREADY transmitting before the prometheus project was approved if Shaw was wrong. I can't find the link, but it was in the viral marketing, but this has The date the planet lv-426 is discovered. The disagreement is so strong, the Elders put a battleship near LV-426 and shot down the the juggernaut before it left the Zeta 2 Reticuli system and it crashed on the planetoid.

6:Since the planet they find in Alien Covenant is the homeworld, and it's a ghost town, something serious happened. I think the Engineers beat the Elders, and that's who David and Shaw meet.

7: This is my speculation based on what I saw in the trailer and stills I've seen. The beluga morphs are black goo+ engineers propagated. David and Shaw released the black goo on the engineer home world intentionally or unintentionally after interaction with the inhabitants.  The chaos that ensues results in the xenos we know and love being released and adding to the chaos. That's where Alien Covenant picks up.