The infamous sequel Alien 3 has plenty of story issues, but the movie’s biggest plot hole is failing to explain how a Xenomorph egg ended up aboard the Sulaco. Directed by future Se7en helmer David Fincher, 1992’s Alien 3 is one of the most divisive entries into the franchise that launched with Ridley Scott’s “haunted house in space” classic Alien. Darker, bleaker, and less action-oriented than James Cameron’s 1986 predecessor Aliens, Alien 3 upset loyal viewers, general audiences, and even its director has effectively disowned the sequel.
Alien 3 was a casualty of a tortured production process that saw the producers reject numerous impressive scripts - including a draft from Neuromancer author/cyberpunk legend William Gibson - before cobbling together a sequel that utilized elements from all of them. Critical reaction to Alien 3 was somewhat brutal at the time of release, with the movie's oppressive tone and the deaths of major characters being two commonly cited complaints. The overall reception to the threequel has thawed over time, however, with some considering the movie vastly underrated and praise it for taking bold chances with the series.
Since Alien 3's script was essentially Frankensteined together from multiple drafts and was being constantly rewritten during production, it's little wonder it features some egregious plot holes. It starts with the most glaring, with the sequel’s action hinging on the presence of a Facehugger being aboard the Sulaco, but without offering any logical explanation of how an egg came to be on the ship. Even decades after the release of Alien 3, there is still no clear explanation and it seems this question will likely never be answered.
The obvious implication is that the Alien Queen planned the egg during the finale of Aliens, but revisiting that climactic scene it's hard to spot a pause in the action where she could have laid an egg. She likely couldn't have laid one without her ovipositor and even if she could have, Alien 3’s Facehugger appears to have been hidden in the ship’s depths, even though the dropship's undercarriage is the lone place she could conceivably planted it. Obviously, for Alien 3's action to happen an egg needed to have been left on the ship somehow, but it feels like the screenwriters simply gave up on conceiving of a plausible explanation.
Various alternate theories have been drawn up over the years, including the idea Bishop (Lance Henriksen) was secretly programmed to steal an egg, but again, the sequence of events seen in Aliens and Alien 3 doesn't really support that reading. Tracing the development of Alien 3's screenplays, it's almost possible to see how this plot element was handwaved away with each successive draft. William Gibson's script revealed an egg grew inside Bishop's intestines within his hypersleep pod thanks to the Queen having infected him with a Xenovirus, while writers Eric Red and Vincent Ward's later drafts offered no explanation for the Xeno outbreaks aboard the Sulaco.
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