Spoiler
"The spaceship Covenant is transporting frozen embryos to a human colony on a faraway planet when they receive a distress signal from Elizabeth Shaw (Noomi Rapace), from the Prometheus expedition, which disappeared 10 years prior. The crew is brought out of hypersleep to answer to the signal, which leads to the death of the Covenant's captain, Branson (James Franco). His wife, Daniels (Katherine Waterson), is deeply affected by the accident, while Branson's first officer Archer (Billy Crudup) is made captain. The Covenant is piloted by Daniels's friend Tennessee (Danny McBride) and the crew is aided by an android, Walter (Michael Fassbender).
The Covenant follows Shaw's signal to Paradise, an uncharted forest planet and homeworld of the Engineers, the ancient extraterrestrials that seeded life on Earth and then sought to the destroy it. The Engineers' secret weapon, the black ooze, has spread through Paradise, turning it into a wasteland. The Covenant's crew ventures outside their ship and some of its members are exposed to spores released by plants infected by the ooze. It is determined they've contracted an alien pathogen and Archer has them quarantined aboard the Covenant.
Monstrous creatures known as "Neomorphs" burst from the infected crewmen's bodies and begin slaughtering the crew, forcing the survivors to flee into the forest, where they are rescued from the Neomorphs by David (Michael Fassbender), the sole survivor of the Prometheus crew. He reveals that Shaw sacrificed herself to crash a spaceship against Paradise's surface, exposing the Engineers to the black ooze to prevent them from destroying Earth, leaving him stranded on Paradise.
David leads the survivors back to the Engineers' derelict citadel, where he's been living ever since. Walter mistrusts David, who is not behaving in accordance with their programming, and finds out that David in fact murdered Shaw. David's mind has been warped by the numerous modifications that his creator, Peter Weyland (Guy Pearce), made to his programming during the Prometheus's expedition, and is obsessed with creating the "perfect organism". He exposed numerous lifeforms on Paradise, including Shaw, to the black ooze and, after numerous failed attempts, has created an alien egg, which produces a facehugger that latches itself to Archer, leading to the birth of a Primal Xenomorph.
Daniels and Tennessee realize David is controlling the Neomorphs and escape back to the Covenant with Walter in order to leave Paradise. Together, Daniels and Tennessee manage to kill the Primal Xenomorph and the Neomorphs and detonate explosives to destroy David's laboratory, with David himself apparently perishing in the explosion.
After escaping, Daniels and Tennessee place themselves back in hypersleep to continue their voyage to the colony, unaware that David has killed Walter and stolen his identity to leave Paradise. David secretly plants two alien egg embryos among the human frozen embryos that the Covenant is transporting to proceed to the next phase of his experiment.
Possibly the next movie will show how engineers were not THE benevolant higher power beings we wanted them to be,they were just a race being pawns of another higher race or higher power but stronger and a lot more advanced within the same race.The engineers we see in lv 223 and 426 are not the same we will see in covenant. The covenant ones are not as advanced...they are like a "primal indigenous" version of the true engineers who mastered the black goo chemical,this engineers are evil and the next sequels will cover more about them and what the black goo is trully capable of,i heard the idea we will follow is that the xenomorph as we know it was never the ultimate organism just one of the variations of the very first "creature" the chemical was made off, at this moment we see the xeno as the big bad beast(queen mostly) but i believe we will have another one to worship as the true perfect organisms.
