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*SPOILERS AHEAD*
The alien threat in it's early stages is air born, like a pollen. Nothing happens until one person gets sick and is carried to the med bay. That is when something VIOLENTLY bursts from the sick man's back and attacks a peer.
From that point it's like the feeling of screeching metal getting louder, standing your hairs on end, as the woman tries to fight off the new born and ends up blowing the freak'in ship up she's in.
Let me vocalize the experience, "Blah nothing..., hm..oh, oh no, ARUGH!? OH GOD! SHIT!! -Anxiety, explosion-"
So now that things get interesting you find out that the fields are crawling with new borns. A stranger however saves them which happens to be the android David from Prometheus.
Here is what you missed in the gap from the end of Prometheus to Covenant. David arrived on a engineer's world and committed genocide with the alien ship Elizabeth Shaw and him had flown away in at the end of Prometheus. It was the same weapon the engineers were on their way to Earth with to wipe out their creation, humanity. They had been mysteriously stalled though which is how Elizabeth and her peers stumbled upon the secrets of man's origins. Where they also discovered that their creators may not be benevolent gods.
Anyway David had been experimenting, including with (the now dead) Elizabeth whom he had apparently turned on. David is one of the old models of androids which could think a little bit more human-like with ambition, creativity, ect.
He basically developed into Ultron and began cultivating life on the world he commited genocide on. The life being the evolution cycle of the species they crossed in Prometheus. He no longer has respect for humans, we wants to craft something more advanced.
When the fresh characters of Covenant begin catching on that this android has sympathy for the beasts and values them more they freak out. David even lures people into being test subjects for things like the newly invented face hugger. Yes, Alien Covenant explains the origin of the face hugger, it was apparently created by a insane A.I.
Who saw that coming? Sit down and stop lying.
Anyway, there is a series of a few fights, more Xenomorphs but like adult size get into the mix.
The humans are trying to escape while the newer model of David fights the old free-will inclined model. It teases you though, as you don't know which one walked away from the fight.
The winner even helps the humans escape from a adult sized alien on their craft during evacuation, so you really aren't certain about anything.
But when everyone gets back into their cryogenic pods to sleep, the main character discovers too late that it isn't their David. It's because while her pod began operating she mentioned something personal she had shared before and the new David hesitated not getting the reference.
Terrified she went to sleep.
The ship and thousands of sleeping humans were under David's watch, he even stored some alien and face hugger embryos in storage with the human fetus tissue.
So extremely amazingly written. Boring opening, not enough about the engineers. It seems like the director refuses to spoon feed answers what's so ever, a lot of it is just completely up to the imagination, forever mystery.
Don't give up on this movie because of the beginning, it's worth sticking to it.