Our versions of the Shaw and David storyline between Prometheusn and Covenat

I say Shaw piloted the ship as instructed by David, but then reluctantly had to re-attach his head and body, to maintain the ship while she went into cryo-sleep for the long journey. Of course, David was one step ahead: he tampered with Shaw's cryo-tube, inducing a coma ready for him to exploit for his experiments later. In the intervening years, he traveled the galactic neighborhood in search of lifeforms to lure into his black goo experiments, and the new film catches up with him when he has finally cocooned Shaw and had a breakthrough with his new life form.

I still can imagine David manipulating her and eventually experimenting on her. We have been given much information, but RS is really holding the Shaw card close to his chest.

I don't think David would hurt Shaw. I think her DNA was affected by contact with the black goo through Holloway and she will undergo unforseen changes.

I wonder how many flashbacks of Shaw and David's journey will be shown. Whatever happened to Shaw will definitely be a big surprise, as Ridley didn't want people knowing she was even in the movie. 

I agree with @Svanya, David has quite a fixation/fondness for Shaw, I have trouble imagining him harming her. Unless of course his studying of the engineer's technology became his top priority. (Crew Expendable)

Shaw might well have tampered with David, and perhaps her tampering resulted in more pronounced personality characteristics than she wanted.

Im with stan, that shaw had to reattach david due to her needing a pilot while she cryosleeps.

But after entering the planet, they make contact with the engineers: who may have changed their ways and reverted to a culture who has abandoned technology. The engineers believe shaw and david (unaware who is piloting the ship) are the return of the group of engineers from the zeta2reticuli star system, who, 2000 years ago left paradise with the mission of going to earth to wipe out any organisms that may pose a threat to them and to colonise the earth for their new home. So these baldy bastards have been waiting 2000 years for them to return. 

But when they are contacted by these humans they realise something has gone wrong and refuse to answer shaws questions or do answer but not the answers she wants. David fears another situation again that may result in war so he destroys them against shaws wishes and she hides from him as he lands. 

She then makes a leg for it mistrusting david and fearing for her life after realizing david is no longer just a robotic programmed tool, but a self aware, thinking and emotional sentinel being. 

I also do think that Shaw isnt behind or agrees with the bombardement.

Either she is in cryo sleep at that stage. My personal guess as well. Or she is already dead.

Personally i think she will witness or learn about what happened after the crashing of the juggernaut happened. Maybe she wakes up alone in the juggernaut ship after it had crashed. First looking around for the search of david. Than checking the computer(engineer desk for logs what has happened prior to her waking up) there she finds out about the bombing. 

Well after that maybe she is looking around the ship for the search of david, dropping the dog tag and may find him either getting knocked out by him and no further explanation or seeing any kind of alien lifeform (neomorph/xenomorph) getting chased and hide out locked up in cryo sleep chamber also no further scenes and explanation.

Point being i think we either see her getting killed or we wont see on screen what ends up being her fortunate.

All of her scenes, which are just a very little quick few ones will most likely be via hologram. With probably her fortunate being the audiences own guesses to make out. Cause the hologram is (maybe intentionally) crubbed or not fully working anymore to show the whole sequence.

I also think it is possible that Juggernaut ship dropped the payload automatically when arrived to the destination point! Because it's a military ship. We all remember that juggernaut ships on LV-223 were heading to Earth to destroy ecosystem. Maybe David had changed destination point, but he didn`t know that ship will attack automatically.

I don't think that Shaw was sleeping in cryo pod when ship arrived. Notice that 10 years passed between Prometheus and Covenant, and David`s hair has grown long while his being on Planet 4. So, their flight from LV-223 to Planet 4 was not too long. Maybe Juggernaut has hyperdrive system. Cryo pods might be just for waiting between missions, standing on a LV-223 base.