I would Label this Thread with SPOILER...
For now i am going to mention Key Elements/Scenes that are in the movie, none of these are 100% Spoilers as they are information we have available from Trailers, Comments by Cast/Crew and Set Reports.
The Order may not be like this, so this is a example.
1) Prologue Scene between Weyland and David (discus about Creation, Perfection, Death, Gods, Mortality and Immortality).
2) Covenant Ship in Space, and then some Event that causes them to have to come out of Cyro-sleep. Possibly explain why Oram (Crudup) becomes Captain.
3) The detection of a Signal of Human Origin that comes from David/Shaw and you can bet the New Captain decides to go there instead of their intended destination.
4) Have scenes of the Crew interacting as they arrive at Paradise, which will no doubt be a way to introduce us to them and also include Daniels and Walter in the Terraforming bay. And then lead to Daniels Questioning the Decision of Oram.
5) The Drop Ship departs for the Surface and then they land and discover the Wheat Field and notice there are no signs of Life.
6) The moment Rigby is infected by the Spores
7) The crew make their way up the Mountain Side but then Rigby becomes ill and he is taken back to the Drop Ship.
8) The moment the crew then head up and enter the Juggernaught, while we flash to Rigby (Ricks) being brought back. Then back to discovery of Shaws Dog Tag and Hologram.
9) The whole Medbay Scene which would include Farris trying to get hold of the Crew, and also Covenant (maybe being ordered to Quarantine Rigby). And then the Back Buster Attack.
10) Takes us to a scene where likely they leave (or some do) the Juggernaught and at this point another crew (Hallet or Ledwood) member is infected and we see the other Spore Infection.
11) Oram then realizes what is next and leaves to the Drop Ship as fast as he can with Rosentnal and Ankor only to arrive as Farris Blows the Ship up.
12) Maybe* Daniels, Walter with either Ledwood or Hallet (bets on Ledwood), Lope, make there way to the Cathedral first by finding Dead Engineers and then they enter the underground Big Head Room.
13) Maybe* Some of the Crew are attacked in the field (Oram Rosentnal and Ankor but are rescued by David).
*Maybe these scenes happen in either order.
14) Oram and Ankor are taken on a guided Tour of where David is held up, while Rosentnal is cleaning her wounds and she is attacked by a Neomorph or something else and screams. As this is happening Ankor goes back maybe?, while David shows Oram all of his Experiments and takes him into the Cave with the Eggs and gets him Face Hugged, then Ankor runs into the same room fends off a Face Hugger and runs into the Work Shop to be attacked by a Xenomorph* (he could be running back as he hears Rosentnal scream).
15) Daniels, and Walter with Ledwood and Lope are ambushed by Aliens and make it to the Cathedral, where they find David.
16) This is where a lot of shots we not seen happens, and between Walter and David before we get the Flash Back of what happened to the Engineers. (but we could get this from David before the Aliens attack).
17) We see the Chest Buster.
18) Back to what ever David, Walter and Daniels are up to.
19) They make their escape after finding out David is up to no good, and call in the Covenant for a Rescue. Lope, Walter and Daniels fight off Aliens. Lope gets killed.
20) Tennessee comes to rescue but Daniels has to fend off a Xenomorph on the Cargo Loader Ship.
21) Daniels, Tennessee and Walter arrive on the Covenant and think they have put the events past them. And we see a moment of reflection.
22) Cole and Upworth decide to take a Shower and make out, as Daniels, Tennessee and Walter decide to leave Paradise and head to their Original Destination. Cole and Upworth are attacked in the Shower. Daniels and Tennessee try and contain the Alien and Walter/David is trying to contain it by controlling the ships Doors to corner it.
23) We have them try and blow up the Alien but it causes a breach, they have to Suit up and then head to the Terra-forming Bay, where Eventually they rid of the Alien.
24) The survivors are relieved and ask Walter/David if the Coast is Clear, and he confirms its now Safe.
25) We get the survivors prepare for their next journey and then we may get a Plot Twist and Set up Ending.
I think we could be seeing 2-3 more Scenes on-top of that and so of these 25 Scenes/Events i think 23 of them we are all ready aware of for sure.
So the Trailers etc allowed us to piece together SADLY 70% of the Movie.