On March 17, 2012, Scott said that the film leaves many questions unanswered and that these could be answered in a sequel. He said, "If we're lucky, there'll be a second part. It does leave you with some nice open questions." Asked whether a sequel would be a direct prequel to Alien, Lindelof said: "If we're fortunate enough to do a sequel ... it will tangentialize even further away from the original Alien." In June 2012, Lindelof said that while plot elements were deliberately left unresolved so that they could be answered in a sequel, he and Scott had thoroughly discussed what should be resolved so that Prometheus could stand alone, as a sequel was not guaranteed. Scott said that a sequel would follow Shaw to her next destination, "because if it is paradise, paradise cannot be what you think it is. Paradise has a connotation of being extremely sinister and ominous." Lindelof cast doubt on his participation, and said, "if [Scott] wants me to be involved in something, that would be hard to say no to. At the same time, I do feel like [Prometheus] might benefit from a fresh voice or a fresh take or a fresh thought." Scott said that an additional film would be required to bridge the gap between the Prometheus sequel and Alien.
As of August 1, 2012 Fox was pursuing a sequel with Scott, Rapace, and Fassbender involved, and was talking to new writers in case Lindelof did not return. The film would be scheduled for a release no earlier than 2014. In December 2012, Lindelof had decided not to work on a sequel, citing other commitments. In June 2013, Jack Paglen was in negotiations to write the sequel. In October 2013, Scott confirmed that the script was complete, but in March 2014, Michael Green was hired to rewrite Paglen's script.
In 2013, a comic book series was announced by Dark Horse Comics that serves as a spin-off to Prometheus. The series, titled Fire and Stone, is a crossover between the Alien, Predator, Alien vs Predator, and Prometheus franchises. The first issue of Prometheus: Fire and Stone was released in September 10, 2014.