Q17. Are there any secret societies with sinister agendas I could join and/or fight?

How about we do this list-style? Just a sample of such societies.

Aelonia (not really secret)

•  The Righteous Order
• A society of do-gooder Adventurers who protect and serve the greater good
• Technically an auxiliary society in support of the Righteous Knights
  
• The Righteous Knights
• An order of paladins focused on defeating evil
• For most people, the Knights are the face of the Church
• Knights of the Order
• An order of paladins focused on defeating Chaos
• Many fewer in number than the Righteous Knights and not much involved with the Righteous Order
• Have never lost a battle in the thousand years since their founding
• The Order of the Open Hand
• More commonly known as the White Guard due to their white sashes
  
• An elite force that provides security within the Church
• Each member is an excellent swordsman who has sworn never to raise a weapon against another
• The Knights of the Chalice (mostly secret) 
• An elite order of Knights who venture into the Abyss to cull demons and gather intelligence
• Once numbered about 100, now only 12 or fewer can meet the strict requirements
• The Eyes of He Who Knows the Hearts of Man (secret)
  
• A secretive order of paladins within the Righteous Knights who serve as inquisitors within the Order and the Church
• They have an ability to detect evil that far surpasses the average paladin
  

Fortune

• Red Lotus
• A society of monks who seek to understand and explore the mysterious powers of ki
• White Lotus
• A rival society of monks who stole secrets from the Red Lotus but misunderstood Ki to be a god; they have developed their own understanding of ki powers
• The Travelers
• A very loose network of adventurer devotees of Derrgan spread throughout the settled lands; they are aware that Derrgan wanders the land and seek to aid his aims whenever possible

Valor

• Black Scorpions
• Not the largest thieves' guild in Valor but certainly the robust up-and-comer seeking to displace and replace
• Acquisitioner's Consortium Auxiliary
• Originally founded as a legitimate business venture to raise halflings out of poverty, a faction of the AC runs its own thieves' guild separate from the main business

Wyndhaven (Chaos Cults)

• Cult of the Ebon Hand
• A group that worships physical deformity as gifts from the gods of Chaos; they openly run orphanages and hostels for the deformed under the guise of charity
• Faces of Fear
• A splinter group from the Ebon Hand that believes self-mutilation is superior to deformity; led by a self-professed Prophetess who declared the Ebon Hand heretics
• Sons of Wrath
• A group that worships strength and violence for their own sake; they terrorize the city with sudden attacks of self-destructive rage; led by a dwarven cleric whose speech can whip his followers into a frenzy
• The Drowned
• A group that worships unknown powers from the depths of the ocean; they hold parties and festivals from which they kidnap victims seemingly at random; these victims are repeatedly subjected to the Drowning until they die or they finally hear the voices of the unseen lords

Duchy

• Fangs of the Wyrm
• The forces rallying around the Dragon Prince
• The Thorns
• Possibly the oldest group here, the Thorns began as a secretive resistance movement when Horde first attempted to conquer the world. Their numbers dwindled precipitously after his death and the Abyssal invasion but the Thorns remained to harry unjust rulers down to the present day. Since the rebirth of Horde, they have found many new members and a faction led by a bard named Rose has taken to openly advocating for resistance and rebellion.