OK - this could be a tough one, but ...

• The Players ( now 3rd level ) ran across a shrine of a cult a few sessions ago ( at 1st level ), and got into a fight with them, killing several cultists, and desecrating the shrine.
• The cult is tied to the "big evil reawakening in the world" - well, maybe not evil, but they do kind of want to re-assume dominance over the world and re-enslave humanity. They are predicted to be the 20th level campaign finale opponents. 
• The cult has tried to assassinate member of the Party once or twice - although only one attempt can be conclusively tied to the cult.
• They are going to try and kidnap the NPCs which are friends to some of the PCs, since the PCs seem to have wandered off and left them unprotected,  in an attempt to lure the Party into a trap.

So - they're acting pretty Evil. 

However - the local cult is tied to a much larger organization, which isn't acting as evil.

The larger organization is based in the capitol city of a rival nation to the setting where the Players are based. One high-level member of the organization is presenting himself as a trader captain. He's in town to arrange for the theft of an important artifact; in fact the plot to steal the artifact, and it's consequences is what drew the Party together. Yes, when the plot went south and the Players managed to detonate explosives in the catacombs beneath the Fortezza Vigilare and collapse the tunnels rather than allow entrance into the basement levels of the Fortezza, the larger cult organization decided to wipe the operation, recover the documents  they lent to the team trying to breach the Fortezza ( and which the Party captured, and then turned over to the Magisterium, even though the Party tinkerer made copies ), and wipe out the witnesses.

They're still working on taking out the operative they hired ( indirectly ), but he's in Magesterium custody since the Party rescued him, and turned him over the authorities - but there's a prison transfer coming up in a day and half ... they'll attempt to strike then.

And, of course, the other re-awakening force ( of course, ancient enemies of the "evil" force ) in the world has contacted the Party as well ... but apart from giving the Party a weapon and a lot of cryptic clues, they haven't gotten as involved yet.

So - the problem is that the actions of the two cult organizations have been pretty unrelentingly hostile, and evil.

I'd really like to start spinning things a little more morally grey.

Right now, there are a lot of local factions involved in the current events ( two rival criminal organizations, an aristocratic family, the city government, and an order of powerful mages acting as unofficial guardians of the city, the local chapter of the cult - and possibly, soon, the parent organization ), and the culmination of this arc will put them all in direct confrontation ( they all want that operative being transported ), with the Party being the "swing vote" - essentially presenting the Party with a need to pick a side, and see which side of the larger campaign conflict they'll be involved with.

So ... I can either start introducing aspects of the factions that have been acting hostile to make them more morally sympathetic, or making the neutral/aiding faction more "evil" - or both.

Ultimately, I'd like the desirability of either side winning the upcoming campaign conflict to be morally grey, and a choice of the Party - even so far as having them oppose both ancient forces be an option.

Any ideas, or general techniques, I might use to making the morality of the situation more murky? 

Some initial thoughts:

• The Cult can try and recruit the Party - offering them power and influence to aid the Cult, and they will kidnap the NPCs not to lure the Party into a trap, but to bring them to the negotiation table. Not so much making the Cult less evil, but an attempt to move the Party morality more in line with theirs.
• Casting the Cult as trying to protect Humanity through accommodation - maybe misguided, but a better motive than worshiping evil to get ahead.
• Casting the Cult as secretly aiding a faction within the "awakening evil" which is more sympathetic to Humanity ( such a faction actually exists, and is meant to be an internal struggle somewhere around level 15 of the campaign ).

The last two are all pretty high-level though, and don't change the Cult's moral appearance much in the short term.

Any other ideas or techniques?

Thanks,

I love adding a bit of ambiguity to the motivations of various factions.  It leads to a lot of interesting character decisions.

So, if I am understanding things correctly, the players know:

• They have fought an "evil" cult
• The cult has tried to assassinate one party member

They DO NOT know that:

• what the cult motivations are
• that they will try to kidnap friendly npcs

Also, based on your description there are a lot of moving parts in this scenario.   Perhaps a few sessions where you focus (or the party goes) to explore one or two factions at a time. Each one will then have a different point of view.

A few thoughts:

• Have the party discover that some of the NPCs that have helped them, or that they are friendly with are members of some of the factions.
  • See if the party will choose to help their "friends".
• Have some of those NPCs approach the party for "help" and potentially send them on "errands" which can lead to moral ambiguity
• Find a way, whether via book/person/divination  (good roll at a tavern) of seeding some information to the party that lends them to think that not everyone within the "evil" organizations are all bad.   Attempt to create a personal connection.  Ie the tavern bartender was once saved by a member of one of the organizations and regards them as a trusted friend.  The bartender may not even know they belong to the organization, but the party may.
• Adding to your 2nd point:  Provide information so that some of the members of the organizations feel they are serving a "greater good".  
  (ie if we do these horrible things, and hurt some people, then those remaining may be saved).  Is saving the world worth 10 souls, 100, 1000? etc. I think you can introduce some of that early, perhaps through an organization member that the party has captured?

Hope some of that helps!   And it sounds interesting :)

Getting the party to not always attack at first sight is often a challenge.

Thanks for the feedback :)

There are really 2 or 3 related layers of factions here.

There's the top layer: the world shaking "great powers" that are awakening - the Party has nothing to do with these directly, and possibly won't until around level 13, if ever ( campaign might not last that long ).

There's the "local agents" of the awakening powers - this being the cult(s), and the benefactor faction. They've mostly interacted with the cults, as adversaries. Tonight's session will likely pull in elements of the Benefactors faction today as "cavalry" if the Party decides to throw down with the main body of the local cult to get their friend back.

There's the "locals" - those factions in the city which are involved in the current adventure arc, which aren't really part of the main campaign conflict, they're just involved in the events which have been precipitated with the Party getting tangled up with the Cult and the Benefactors. These would include the two rival criminal factions ( one hired by the cult to steal the artifact, one hiring the Ranger to assassinate the leader of the expedition to steal the McGuffin in the fortress - for good reasons ), the local police/government, and the fraternity of Wizards who informally look out for the city's well being ( including one of my wife's wizard's former teachers ).

Eventually the setting of the campaign will migrate away from the city that they're currently in, and thus they'll leave most of the locals behind.

If you're familiar with the show, the fictional war I'm using as an inspirational pattern is the The Second Shadow War from Babylon 5  :D

So, if I am reading your advice correctly - thank you! - it boils down along these lines?

• Show that the "bad" guys have motives that are actually positive - trying to achieve a positive result in an untenable situation, so their actions are ( by necessity ) appear to have other motives: ensuring survival through cooperation, or working with in an attempt to influence or control the awakening power ( sort of Mass Effect there ). It could even be that the lower "local" faction is purely evil, but the larger organization has morally sympathetic motives.
• Show that the actions of the "good" guys sometimes have morally questionable results - again, working toward a "good" result with morally questionable shortcuts ( numerous war time decisions made by any side in any war ).
• Build up "good" and/or "bad" NPCs, and then reveal them to attached to factions - morality of the group through association with individuals the Party has already judged,  Better yet good and bad agents attached to a faction. Think of Fallout 4 here where Kellogg and Shaun are both part of The Institute - and the Sole Survivor has pretty clear ( initial ) impressions of their morality.

That's helpful, thanks! :)

I think having some contacts from the mid tier factions reach out to the party to explain to them the situation as they know it and the reasoning for their part in the plot so far (we asked them to obtain the McGuffin and they said that they could do it.  If we knew that they were that evil, we would have considered other avenues first and have realized that we need to vet our futures allies better. We release your allies as a show of good faith, this truly shows that we can't trust the judgment of {evil cult name here}. I'm just happy that we mobilized after the disaster at the Fortezza so that we could forestall any further disasters at their hands.) Each side of the conflict could bring up similar regrets about actions and praise the party for their part in preventing "an even greater travesty" from occurring. I could see these mid tier organizations having contracts that are established nobles or other high ranking officials in neighboring cities who are self important enough to use language that was a little more flowery and pompous. However, that may also lean a touch more towards a seemingly evil and perhaps less approachable organization than what you want, so if you like that idea but want to keep it real, you could have a counterpart within the organization who is accompanying the "pompous windbag" interject from time to time and showing more awareness about the situation, perhaps alluding to the high level reawakening force and painting it in the heroic colors that he sees it in. 

I'm playing a unique approach to one of my games that may prove insightful to your current plight:

The party became unwitting conscripts under the commander of a large armada that traveled across a large and treacherous sea. The party was then told that they're part of an army that is reclaiming this continent, it was origin of the people who lived back home. He sent the party, and a number of NPCs out to gather make contact with the locals and has them acting as emissaries. 

In reality the commander is an exile who is trying to wage a campaign to seize the continent as his own. He's letting the party be heroes in the eyes of the locals to win their trust, then using special means to "persuade" the mayors, thanes, and other rulers to see him as their leader. His ultimate goal is to wipe out opposition, and claim the seat as the lord of the entire continent. 

The trick is to spin everything so the players will view this as their commander having them squash the "bad guys" and continue to see the commander as their benefactor.

---

If you want the morals of the factions to become muddled for your players, give them a reason to trust the factions. Have the factions help them, save them, provide for them, then have them run into pockets of resistance and treachery. Constantly flip the script when you feel the players have concluded that this, or that, faction is "evil" or "good".

Oh, I very much like them claiming plausible deniability of the unfortunate acts of local agents who were acting on their own initiative, and well beyond their authority ( and of course will be suitably punished )!

I can even spin that, since the attack of the mid-tier organization lead with them using sleep against all the house guards, not fireball ( see? we don't want anyone to get hurt ... ).

That means that the mid-tier bad guys can't assault the prison transport as I was thinking - since that's an overt hostile act.

To be honest, they were going full on assault to give the Party some action - but if the lower level tier gives the Party a stand up fight by kidnapping their friends, the Players have had their action.  I was leaning toward the local cult leader attempting to recruit/subvert the Party, but I might kick that up a tier.

I think it could be an interesting cliff hanger scene for the next session being the trader captain / local leadership in the mid-tier organization contact them, or have them "brought in" to reason with.

I think the mid-tier would still try and intercept the prison transport - but they might be less interested in an all out assault. Their motivation is to "clean up" the operation, and that includes the prisoner being transported - but they are foreign nationals from a power with whom Lucana's diplomatic relationships are strained, so, perhaps a subtler approach is called for: restrain, subdue, alter memories ...

That makes them a little more human, a little less directly hostile, and a little more grey.

I can add grey to the "good" guys from the ground up, as they're just now being introduced - having taken an interest in the actions of the Party mostly due to the fact that they're tangling with the "bad" guys.

Thanks! :)

Yup!  I would add that (with B5 references included :D ):

1) "Show that the "bad" guys have motives that are actually positive".

Or at least they feel that their motives are positive.  "Knock over an anthill and it gets better. it improves,  the ants evolve."

2) "Show that the actions of the "good" guys sometimes have morally questionable results"

We could have saved this planet but needed to keep our capabilities secret for now.  (the story of Churchill and Enigma is poignant here)

3) " Better yet good and bad agents attached to a faction"

Nailed it.  It could also be an agent that changes over time, ie G'kar :)   At least to me, you use the same tricks as making NPCs meaningful and likeable so that the party feels a personal connection with them.  From a psychology standpoint, then they are attached and will begin justifying some of the NPCs actions.   An idea would be something like:

Antoinette the local seamstress was walking to the tavern.  The party had already contacted her about possibly making them a flag/emblem/standard.  As she walks she races to a burning building.  The party sees her running out of the building having saved a child.  She's now a hero.  Of course her faction set fire to the building in the first place, but perhaps thought no one was inside.   Of course, the party could have been helping put out the fire as well or be on their way to it so that they are not completely passive observers.

I liked JHffan's take as well, with having the middle tier / brokers be ones that can be more sympathetic.  That would be the "middle man" from B5

"Each side of the conflict could bring up similar regrets about actions and praise the party for their part in preventing "an even greater travesty" from occurring."

@DMThac0 - I like the flipping the script idea. Sure, the "bad guys" were attempting to loot a relic kept under wraps by the government of Lucana , and have committed some violent acts to get it - but maybe the artifact is needed for something important ( stealing from Matt Mercer, here ).

Sure, the local cadre of Wizards are merely trying to protect the city and are trying to suppress the actions of Sassanan national agents in the city - but they're operating outside the law, and without oversight, and might take a few moral shortcuts, as they wield power without oversight ( and this raises possibilities of of Lawful aligned resistance from within the government; two "good" factions which are at odds ).

@Koradgee - I rather like the idea of an agent that changes. Set up an NPC as a mid-level Villain, who "reforms" ( at least from the perspective of the Party's morality ), and with whom the Party needs to now work in order to achieve and important objective.

I will need to hold the whole "Coventry affair" idea in my back pocket and see if I can work that in! :)

 This might be getting so morally grey that I don't know who the good guys / bad guys are :D

Which is how it should be - it's the Party that gets to decide.

The wizards as a "good group" that has great power and operates outside the law harkens to Captain America: Civil War. From there, a little leg work makes the equivalent of SHIELD look more like HYDRA, particularly if your players are invested in the MCU. Which brings up another possibility, have a doppelganger be an agent of the "good" faction. Doppelgangers almost always have an evil connotation associated with them and just the presence of one can muddy the waters there. This can be countered on the other side by an "Ethan Hunt" moment where one of the NPCs that were abducted is imitated by a disguise expert saying that the rest of "his/her" friends are in trouble and the party needs to come quick. This would be the way that the party responsible for the hiring of the criminal network makes contact with the party peacefully, and helps to build trust with the party. It's an interesting use of tropes within pop culture to manipulate the narrative thus far, but doing it in a way that opens the story up for the party to grab the reins. Of course, you may have to work it a little more if they aren't familiar with those pop culture references.

You liked the plausible deniability approach of the larger organization, that they were unaware of the actions of the local cult. Another option is they are aware of the cult's actions and while they don't necessarily disagree with their approach, they are worried about the negative publicity they are getting from their interactions with the party. Perhaps they try to distance themselves from the local cult and send their own representatives to take over operations in the area. A more diplomatic approach. And maybe they are still cooperating with the local cult in secret. 

Also consider before the players have to make a decision giving examples of the good and bad each side does. With the organization perhaps there was a village that was attacked or destroyed or people who were killed in order to achieve their goal. But the next day they open up a clinic and send resources to heal and rebuild the town. As the players investigate they are told something along the lines of the deaths before were necessary but no longer.

If you want to try to present a good side to them show some of the good acts they engage in without any expectation of a return fro them. When they do something good they don't want to be paid or honored, they don't want to draw attention to themselves. Something that gives the players the sense that if they destroy this organization they will be eliminating a great evil but also the source of so many good acts throughout the lands.

Well - as of last night, the lower level of the cult organization might have a few survivors - between the Party taking out most of the leadership high ( for a 4th level party ) level casters, and the Benefactor faction weighing in to help ( via their spooky patented technique of "possession" of members of the construct species ) - they've been pretty much wiped out.

However, the session ended with the Party walking into their base of operations to find the mid-tier organization's leader there, greeting them ( partly ) with "' ... and I believe that we are at war. I'd like to discuss the means by which we might end that" ( cue weekly credits ).

So next session I get to put all this in practice and see if he can't conversationally tap-dance his way into moral ambiguity :)

I do really like the "our associates erred greatly, but they are now all dead, yes? Perhaps we can compensate, in some small degree, those unfortunates who suffered at their misguided hands ... ", a tactic that kind of aligns with your approach.

Then again - can't turn them into the good guys either - gotta keep them morally grey.

Eventually the factions will have to show their true colors - but what those colors might be could be totally dependent on how the Party approaches the story.

One of my favorite techniques is by making it someone they know. Whether it's a twist villain, or someone starting out as a small fry thug growing to be a awful person. One of the ways you can use this is in a omen situation. This is where the party meets someone who is on a conflicted path, such as a warlock struggling with the morals of his pact. The players meet him and befriend him. Then they hear of an omen telling of how he will become a monster and kill hundreds. The party or an npc try to kill the warlock the prevent the coming of the omen, but in doing so set him on a path of evil and vengeance. This is a self fulling prophecy, where the players or npc would feel some responsibly for creating him into the villain.