Over at the Vaults of Pandius there's a really solid article and battle map on the Caves of Chaos from B2 The Keep on the Borderlands by Gary Gygax by Darren Moffett. He makes an excellent point about his own experiences with B2; " My main Adult Campaign has been running a sandbox around the Town of Threshold and the Characters took the hooks for some things and not others. My Kids campaign consists of whatever the Adult campaign decide not to do. I modified the kidnapped girls scenario from Thorns Mystara to fit my own ideas. The first few Game session with the adults the kidnappings were happening behind the scenes mostly, as they explored the Sewers, the Old mill and Killed a Hag and Rescued a Druid." This blog post picks right up where this one left off.
The old religion in T1 The Village of Hommlet has been pushed out & the newer faith is taking hold. Could the old religion of the druids actually be the remains of the Warden's ecology sciences department. And the new St. Cuthbert be part of the old command & control group aboard the Warden?! Sure they could but whose behind the Cult of Chaos?! My guess would be some of the colonial forces aboard the Warden. Little by little a serpent has been winding through the lands of the generation ship. Maybe Robert H. Howard's Set or another Lovcraftian Chaos god is behind the shrine of Chaos in the cavern works in section 'K'. Where did the humanoids come from?! The Warden is churning them out itself! The Warden maybe subject to dark forces as the humanoids rage across the land. The Starship Warden has been on its journey for quite sometime now looking at the Starship Warden rpg book. Personally there maybe a door that the cult of chaos is guarding leading into the bowelsof the Warden. Reading through B2 the cult of chaos is very powerful even though this is a beginning module. They are motivated, have access to magic, & the blessings of their evil masters. So where are their evil masters?! For the Starship Warden perhaps on another deck entirely. Each deck could well be considered another campaign realm entirely. Corrupting the hearts & minds of your enemies is a long staple of Science Fantasy. And these dark powers of B2 have multiple agendas working at the same time. Not even the high technologies of the Warden maybe enough to hold this at bay. The OSR Grimoire blog has an excellent entry from April 2021 that hits on a high point and takes in a bit about the cosmology of Paul Anderson like nature of Law & Chaos within B2; "Much has been written suggesting the American frontier as the ideological framework behind D&D in general, and "The Keep on the Borderlands" in particular, (see comments for this post from Grognardia as far back as 2008, as well as this post from Blog of Holding in 2016).
The Realm of mankind is narrow and constricted. Always the forces of Chaos press upon its borders, seeking to enslave its populace, rape its riches, and steal its treasures. If it were not for a stout few, many in the Realm would indeed fall prey to the evil which surrounds them. Yet, there are always certain exceptional and brave members of humanity, as well as similar individuals among its allies - dwarves, elves, and halflings - who rise above the common level and join battle to stave off the darkness which would otherwise overwhelm the land. Bold adventurers from the Realm set off for the Borderlands to seek their fortune. It is these adventurers who, provided they survive the challenge, carry the battle to the enemy. Such adventurers meet the forces of Chaos in a testing ground where only the fittest will return to relate the tale. Here, these individuals will become skilled in their profession, be it fighter or magic-user, cleric or thief. They will be tried in the fire of combat, those who return, hardened and more fit. True, some few who do survive the process will turn from Law and good and serve the masters of Chaos, but most will remain faithful and ready to fight chaos wherever it threatens to infect the Realm.
from B2 "The Keep on the Borderlands"
This brings up the point is the fate of the Warden more then simply the fate of a spacecraft on an interstellar journey? Ancient OSR theorists such as myself say, 'yes'. The Warden's journey has at its heart the frontier within a frontier.