Here's what happened to the USCSS Prometheus following the events of Ridley Scott's prequel Prometheus. Following the universally negative reaction to 2008's Alien Vs Predator: Requiem, Fox cancelled plans for a third movie and decided to focus on a prequel to the original movie. One element of Alien that always fascinated fans was the dead Space Jockey creature found in the Derelict, with Scott himself speculating the creature's race designed the Alien as a bioweapon. Scott eventually came on board to direct the project when it was known as Alien: Engineers.
The original script by Jon Spaihts featured the broad story beats of Prometheus, but also included familiar tropes like Xenomorphs and facehuggers. Scott eventually brought Damon Lindelof (Lost) on to rewrite the script and make it more of a spinoff than a direct prequel. The resulting film was one of the most anticipated sci-fi films of all time, but Prometheus proved disappointing to some. Notable problems were characters putting themselves in harm's way for no logical reason and a lack of genuine suspense. That said, the movie also received praise for Michael Fassbender's fantastic performance, the production design and for expanding the lore of the Alien universe.
The next entry Alien: Covenant featured a new cast of characters - aside from Michael Fassbender's returning David - and took place on an Engineer planet. For any fans curious to know what happened to the wreckage of the USCSS Prometheus or the Deacon creature following the events of the prequel, then comic series Prometheus: Fire And Stone provides answers. This series was part of a larger, franchise spanning crossover event, with Predator, Aliens and, Alien Vs Predator all forming part of the Fire And Stone saga.
The bulk of Prometheus: Fire And Stone is set in 2219 where the crew of the Geryon arrives on LV-223. This is where Peter Weyland and the ill-fated crew of the USCSS Prometheus disappeared over a century prior. Instead of the desolate planet seen in Prometheus, the moon is covered in dense jungle and pockets of the Engineer's black goo, AKA the Accelerant. The jungle is also filled with mutated monsters that resemble Xenomorphs, including shark-like creatures.
The planet has a jungle because the USCSS Prometheus crashed into the Engineer ship in the finale of Scott's movie, causing it to spill it black goo payload over the surface. This terraformed LV-223 but there's also a derelict craft from Aliens' LV-426 on the planet that unleashes a nest of Xenomorphs on the Geryon crew, while an Engineer hunts and kills humans and Xenos alike. In the midst of this craziness, an android named Elden is also injected with black goo to test its properties, which rapidly mutates him into a sentient monster that can exert control over the Xenomorphs.
A one-shot comic called Prometheus: Fire And Stone - Omega also revealed the final fates of the USCSS Prometheus and the Deacon. Following the events of the previous comic most of the crew has been wiped out, with the survivors teaming up with a friendly Predator dubbed Ahab. The crew discovers a distress signal coming from the Prometheus and decide to investigate, and tunnel into a mountain to find the source. When a wall starts bleeding acid, they come to the realization the mountain itself is a living entity, which is the result of the Deacon creature merging with the USCSS Prometheus and continuing to expand for over a 100 years.
Elden sacrifices himself by merging with the wall, allowing the others to escape. The Prometheus: Fire And Stone saga told one large, ambitious story while also tying up the loose ends of the Alien prequel. While the revelation that the Deacon became a living mountain that also fused with the USCSS Prometheus is a tad anti-climatic, it at least provides some closure for those who wondered what happened after the credits rolled.